Region 1 Fisheries Documents

Background Compendium and Design Criteria Report for the Feasibility of Volitional Fish Passage above Keswick and Shasta Dams

Mon, 09 Mar 2026 10:19:53 -0700

Fish passage, salmonids - This Project builds on the previous work that has been completed to bring Chinook Salmon back to the Winnemem Waywaket, and the overarching goal of the Project is to collect data needed to inform and evaluate volitional fish passage alternatives. Specific project objectives included the following actions: Reach out to and coordinate with key collaborators and landowners to communicate Project goals and objectives. Incorporate ITEK into data gaps studies, as possible, by collaborating with the Winnemem Wintu Tribe to learn about ITEK and the Winnemem Wintu Tribe's perspective on fish behavior, timing of life-history events (e.g., spawning and migration), and observed traits and characteristics. Provide support to USGS as it implements the biological data gaps project by providing expert knowledge on salmon behavior and ecology needed for fish passage and alternatives assessment. Organize and co-lead a tour of Pacific Northwest (PNW) fish passage facilities in 2025. Compile existing data or collect new data on the information needed for the formulation and evaluation of volitional passage alternatives. Describe the current trap and haul concept for Shasta Dam in sufficient detail to allow volitional passage alternatives to be compared to traditional trap and haul.

2025 Kids Fishing Day at Mount Shasta Fish Hatchery

Wed, 09 Apr 2025 16:26:02 -0700

Outreach -

South Fork Eel River Salmonid Abundance Monitoring Project 2023-2024

Wed, 29 Jan 2025 12:16:33 -0800

California Coastal Monitoring Plan South Fork Eel River - From November 21, 2023 to February 27, 2024, a total of 160 spawning ground surveys were conducted over 33 spatially balanced and randomly selected reaches in the SFER watershed. Each reach was surveyed an average of 3.4 times, and the average interval between surveys over all reaches was 22.1 days. During 2023-2024 SFER monitoring, surveyors observed 95 live Coho Salmon, two live Chinook Salmon, four live steelhead, 32 Coho Salmon carcasses, 14 Chinook Salmon carcass, and 23 unidentified salmonid carcasses. A total of 140 redds were detected, of which 51 redds were observed to be associated with a specific salmonid species while in the field. The remaining 89 redds were assigned a species using a k-Nearest Neighbors algorithm. The number of redds observed in randomly selected sample reaches was expanded to estimate the number of redds constructed across the entire SFER sample frame. Redd abundance estimates for the 2023-2024 spawning season in the SFER, including 95% confidence intervals, were 718 (231 - 1205) Coho Salmon redds, 105 (17 - 195) Chinook Salmon redds, and 106 (31 - 182) steelhead redds.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in the South Fork Eel River, Humboldt County California, 2021-2022

Tue, 24 Sep 2024 11:00:53 -0700

California Coastal Salmonid Monitoring Program, South Fork Eel River, Spawning Ground Survey - The Adult Salmonid Redd Abundance Monitoring Project develops annual salmonid redd abundance estimates in the South Fork Eel River (SFER) to inform conservation strategies for the state and federally threatened Southern Oregon/Northern California Coast Coho Salmon Evolutionarily Significant Unit (SONCC ESU)(Coho Salmon). The survey is designed to capture the entire spawning universe of Coho Salmon in the SFER and provides a complete estimate of the redd abundance for Coho Salmon. Other species such as Chinook Salmon and steelhead are incidentally observed during surveys and that data is used here to generate partial estimates of their respective redd abundances; however, due the spatial and temporal constraints of this survey these estimates do not reflect true abundance nor should be viewed as indices of abundance for these species. During year 2021- 2022 of the SFER Adult Salmonid Redd Abundance Monitoring Project, 265 spawning ground surveys were conducted over 36 spatially balanced and randomly reaches in the SFER watershed from October 27, 2021 to May 13, 2022. Each reach was surveyed an average of 7.36 times, and the average interval between surveys over all reaches was 16.95 days. Surveyors observed a total of 65 live Coho Salmon, 13 live Chinook Salmon, 23 live steelhead, and 11 unidentified salmonids42 Coho Salmon carcasses, 10 Chinook Salmon carcasses, three steelhead carcasses, and 11 unidentified salmonid carcasses. A total of 261 redds were detected, of which 17 redds were observed to be associated with a specific salmonid species. The remaining 244 redds were assigned a salmonid species using a k-Nearest Neighbors algorithm. The number of redds observed in randomly selected sample reaches was expanded to estimate the number of redds constructed across the entire SFER sample frame. Redd abundance estimates for the 2021 -2022 spawning season in the SFER, including 95% confidence intervals, were 941 (498 - 1380) Coho Salmon redds, 155 (44 - 266) Chinook Salmon redds, and 397 (187 - 607) steelhead redds.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in the South Fork Eel River, Humboldt County California, 2022-2023.

Tue, 24 Sep 2024 11:00:42 -0700

California Coastal Monitoring Plan South Fork Eel River - The Adult Salmonid Redd Abundance Monitoring Project develops annual salmonid redd abundance estimates in the South Fork Eel River (SFER) to inform conservation strategies for the state and federally threatened Southern Oregon/California Coast Coho Salmon ESU. The survey is designed to capture the entire spawning universe of Coho Salmon in the SFER and provides a complete estimate of the redd abundance for Coho Salmon. Other species such as Chinook Salmon and steelhead are incidentally observed during surveys and that data is used here to generate partial estimates of their respective redd abundances; however, due the spatial and temporal constraints of this survey these estimates do not reflect true abundance. During year 2022 of the SFER Adult Salmonid Redd Abundance Monitoring Project, 161 spawning ground surveys were conducted over 40 spatially balanced and randomly selected reaches in the SFER watershed from November 16, 2022 to February 21, 2023. Each reach was surveyed an average of 4.1 times, and the average interval between surveys over all reaches was 20.4 days. Crews observed 22 live Coho Salmon, 53 live Chinook Salmon, six live steelhead, and 15 unidentified salmonids. Crews encountered six Coho Salmon carcasses, two Chinook Salmon carcasses, zero steelhead carcasses, and five unidentified salmonid carcasses. A total of 51 redds were detected, of which 11 redds were observed to be associated with a specific salmonid species while in the field. The remaining 40 redds were assigned a species using a k-Nearest Neighbors algorithm. The number of redds observed in randomly selected sample reaches was expanded to estimate the number of redds constructed across the entire South Fork Eel River sample frame. Redd abundance estimates for the 2022 spawning season, including 95% confidence intervals, are 109 (48 -169) Coho Salmon redds, 132 (31 - 233) Chinook Salmon redds, and 5 (4 - 14) steelhead redds.

Annual Report on the Mad River Winter-Run Steelhead Breeding Program and Hatchery and Genetic Management Plan for 2019-2024 Brood Years

Tue, 23 Jul 2024 11:43:27 -0700

Mad River Hatchery and Genetics Management Plan - This report is presented as required by the Hatchery and Genetic Management Plan (HGMP) for CDFW's Mad River Hatchery (MRH) winter-run steelhead program. It summarizes general hatchery operations, hatchery steelhead production, and CDFW's efforts to monitor natural-origin (NOR) and hatchery-origin (HOR) steelhead populations within the Mad River basin. This report covers activities relating to MRH and the HGMP for hatchery brood years 2019-2024 and follows preceding annual reports on HGMP compliance delivered for brood years 2017 and 2018.

Ocean Ranch Restoration Project - Post-Restoration Fish Montoring -Year 1

Mon, 08 Jul 2024 15:15:41 -0700

Eel River Estuary Fish Monitoring on the CDFW Ocean Ranch property - This report represents the first of a five-year post-restoration monitoring program to document and characterize community composition and spatio-temporal distribution of fish species in the restored and enhanced estuary habitat of the Ocean Ranch Unit (ORU). Post-restoration fish validation monitoring is scheduled to continue through January of 2028 to determine if the project was successful in improving habitat conditions for special-status fish and the fish community.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in the South Fork Eel River, Humboldt County, California, 2017-2018

Sun, 16 Apr 2023 19:03:50 -0700

regional salmonid monitoring CMP - The South Fork Eel River Adult Salmonid Redd Abundance Monitoring Project conducted 249 spawning ground surveys upon 37 spatially balanced and randomly selected reaches in the South Fork Eel River Watershed between November 6th, 2017 and February 15th, 2018. Each reach was surveyed an average of 6.7 times, and the average interval between surveys over all reaches was 16.8 days. During the 2017-2018 survey season, crews observed 144 live coho salmon, 114 live Chinook salmon, 8 live steelhead, and 15 unidentified salmonids. Surveyors encountered 11 coho salmon carcasses, 30 Chinook salmon carcasses and 1 unidentified salmonid carcass. A total of 356 redds were detected, and 49 of those redds were observed to be associated with a specific salmonid species digging or guarding the redd. The remaining 307 redds were predicted to species using a k-Nearest Neighbors model. The number of redds were estimated in each sample reach using flagged and re-observed redds in a mark-recapture model then expanded to estimate the number of total redds constructed across the entire South Fork Eel River reach sample frame. Redd abundance estimates for the 2017-2018 spawning season in the South Fork Eel River sample frame area, including 95% confidence intervals, were 1,633 (793, 2473) coho salmon redds, 867 (454, 1279)* Chinook salmon redds, and 5 (1, 15)* steelhead trout redds.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in the South Fork Eel River, Humboldt County, California, 2016

Sun, 16 Apr 2023 19:03:41 -0700

regional salmonid monitoring CMP - During year seven of the South Fork Eel River Adult Salmonid Redd Abundance Monitoring Project, 227 spawning ground surveys were conducted over 40 spatially balanced, randomly selected reaches in the South Fork Eel River Watershed from November 3, 2016 to March 9, 2017. Each reach was surveyed an average of 5.6 times, and the average interval between surveys over all reaches was 19.7 days. During the 2016-2017 survey season, crews observed 102 live coho salmon, 360 live Chinook salmon, 8 live steelhead, and 36 unidentified salmonids. Crews encountered 6 coho salmon carcasses, 102 Chinook salmon carcasses, 1 steelhead carcass, and 9 unidentified salmonid carcasses. A total of 320 redds were detected, of which 86 redds were observed to be associated with a specific salmonid species while in the field. The remaining 234 redds were assigned a species using a k-Nearest Neighbors algorithm. The number of redds observed in sample reaches was expanded to estimate the number of redds constructed across the entire South Fork Eel River sample frame. Redd abundance estimates for the 2016-2017 spawning season in the South Fork Eel River, including 95% confidence intervals, were 465 (98,831) coho salmon redds, 1,458 (923,1,992) Chinook salmon redds, and 54 (9,111) steelhead redds.

Lower Eel River and Van Duzen River Juvenile Coho Salmon (Oncorhynchus kisutch) Spatial Structure Survey 2013-2016 Summary Report

Sun, 16 Apr 2023 17:38:15 -0700

Lower Eel River and Van Duzen River juvenile coho salmon surveys 2013-2016 summary report - Monitoring of coho salmon population spatial structure was conducted, as a component of the California Department of Fish and Wildlife’s Coastal Salmonid Monitoring Program, in the lower Eel River and its tributaries, inclusive of the Van Duzen River, in 2013, 2014, 2015, and 2016.A total of 211 snorkel surveys were conducted on 163 reaches, with 2,755 pools surveyed during the summers of 2013, 2014, 2015,and 2016.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in the South Fork Eel River, Humboldt County, California, 2015

Sun, 16 Apr 2023 17:38:09 -0700

Spawing Survey Results in SF Eel River 2015 - During year six (2015/2016) of the South Fork Eel River Adult Salmonid Redd Abundance Monitoring Project, 190 spawning ground surveys were conducted over 40 spatially balanced, randomly selected reaches in the South Fork Eel River watershed from November 18th, 2015 to March 3rd, 2016.

Summer stream temperature profiles in the Smith River basin from 2009 to 2013

Sun, 16 Apr 2023 14:40:16 -0700

water temperature, water quality - This study monitored the summer water temperature in various tributaries of the Smith River, Del Norte County, California from 2009 to 2013. This summary provides baseline thermal profiles, average, and maximum temperatures and recommendations for future temperature monitoring.

McNulty slough, thence Eel River estuary fish and water quality sampling January 2008 through June 2009

Sun, 16 Apr 2023 13:10:41 -0700

eel river estuary fish and water quality sampling - As a follow-up to water quality and fish sampling conducted in September 2006 and 2007 by the California Department of Fish and Wildlife (CDFW), CDFW conducted additional fisheries and water quality sampling in McNulty Slough in the Eel River estuary. The purpose was to document water quality conditions and to determine if juvenile salmonids are present in the area.

Tidewater goby and water quality sampling Ocean Ranch Unit, Eel River Wildlife Area summer 2012

Sun, 16 Apr 2023 12:33:35 -0700

tidewater goby survey, Ocean Ranch Unit, Eel River estuary - In an ongoing fisheries, hydrology, and water quality monitoring effort to document current conditions and evaluate the potential for tidal marsh restoration on the California Department of Fish and Wildlife (CDFW) Ocean Ranch Unit (ORU) of the Eel River Wildlife Area (ERWA), CDFW surveyed for the federally endangered and California Species of Special Concern tidewater goby (Eucyclogobius newberryi) from June 13 through August 17, 2012. This was the first survey conducted specifically to determine tidewater goby presence or absence throughout the ORU.

Mendocino County salmonid life cycle and regional monitoring: monitoring status and trends for 2012. 2011-12 Administrative Report.

Sun, 16 Apr 2023 12:32:28 -0700

regional salmonid monitoring CMP - California’s coastal salmon and steelhead populations are listed under California and Federal endangered species acts; both require monitoring to provide measures of recovery. Since 2004 the California Department of Fish and Game and NOAA Fisheries have been developing a monitoring plan for California’s coastal salmonids (the California Coastal Salmonid Monitoring Plan- or CMP). The CMP monitors the status and trends of salmonids at evolutionarily significant regional scales and provides population level estimates. For the CMP, data to evaluate adult populations are collected using a spatially balanced probabilistic design (e.g., Generalized Random Tesselation Stratified- or GRTS). Under this scheme a two-stage approach is used to estimate status. Each year regional redd surveys (stage 1) are conducted in stream reaches in a GRTS sampling design at a survey level of 15% of available habitat or a minimum of 41 reaches, whichever results in fewer reaches. Spawner: redd ratios are derived from smaller scale census watersheds (stage 2) where “true” escapement is estimated using capture-recapture methods. These are used to estimate regional escapement from expanded redd counts. In 2008-09 we applied the results of our previous studies to estimate salmonid escapement for the Mendocino coast region, the first implementation of the CMP in the state. Here we present the results of the fourth year (2011-12) of this monitoring effort and discuss our findings in the context of expanding the CMP to all of coastal California. We discuss sample frame development, sample size, and present escapement data for major portions of the California Coastal (CC) Chinook Salmon Evolutionarily Significant Unit (ESU), the Central California (CCC) Coho Salmon ESU, and the Northern California (NC) Steelhead Distinct Population Segment (DPS). In addition, we present 2011-12 data from three life cycle monitoring streams and combine this information with previous years’ data to evaluate status and trends for coho salmon and steelhead.

Identifying factors limiting coho salmon to inform stream restoration in coastal Northern California

Sun, 16 Apr 2023 12:28:14 -0700

Coho Salmon - We evaluated an eleven-year (2000 to 2011) coho salmon adult, parr, and smolt abundance data stream from three census watersheds in coastal Mendocino County, California to determine how this information can provide a scientific basis for directing life-stage specific stream restoration activities. The three census watersheds: Caspar Creek, Pudding Creek, and the South Fork Noyo River called Life Cycle Monitoring Streams (LCMS), are part of the California Coastal Salmonid Monitoring Plan. These LCMS are places where we estimate adult, parr, and smolt abundance; make connections between life stage abundance and abiotic factors; and serve as focal points to foster additional watershed and salmon research. Adult and smolt abundance was estimated using capture-recapture methods where fish were marked with either batch marks or individual identifiers and we estimated parr abundance with depletion sampling. Since 2006, we applied Passive Integrated Transponder (PIT) tags to parr and smolts >70mm and used this data to estimate abundance and survival. We used these data to calculate marine and freshwater survival, estimate carrying capacity of the three streams, and investigate the relationship between survival and abiotic factors (stream flow, turbidity, and temperature). We present the findings of this analysis and our results in relation to habitat census evaluations conducted during summer 2011. Finally, we discuss the application of our findings to restoration using large wood and provide recommendations for future work to increase coho salmon production.

Discrimination of Chinook and coho salmon and steelhead redds and evaluation of the use of redd data for estimating escapement in several unregulated streams in Northern California.

Sun, 16 Apr 2023 12:28:12 -0700

Coastal salmon escapement monitoring - I developed and evaluated a stratified index redd area method to estimate Chinook (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) and steelhead (O. mykiss) escapement in several coastal streams in Northern California based on the assumption that redd size is related to the number of redds a female builds. Sources of error in redd counts were identified and reduced including the use of logistic regression to classify redd species, necessary due to temporal overlap in the spawning of these species in coastal Northern California. Redd area escapement estimates were compared to estimates from more conventional methods and releases above a counting structure. Observer efficiency in redd detection ranged from 0.64 (S.E. = 0.10) to 0.75 (S.E. = 0.14) and was significantly associated with stream flow and water visibility (ANOVA f = 41.8, p < 0.001). Logistic regression significantly reduced uncertainty in redd identification. Redd area and date observed were significant in predicting coho salmon and steelhead redd species (Wald’s z = 11.9 and 18.09, respectively, p < 0.001). Pot substrate and redd area were significant in classifying Chinook and coho salmon redds (Wald’s z = 5.88 and 4.03, p = 0.015 and 0.04, respectively). Stratified index redd area escapement estimates and capture-recapture, area-under-the-curve, and known releases above the counting structure (coho salmon only) were not significantly different (ANOVA f < 13.6, p > 0.06). Escapement estimates assuming one redd per female were only significantly different from other methods for steelhead (ANOVA f = 13.11, p = 0.006). Redd counts were significantly correlated with escapement estimates (r > 0.82, p < 0.04). Reduction of counting errors and uncertainty in redd identification, biweekly surveys throughout the spawning period, and the use of redd areas in a stratified index sampling design produced precise, reliable, and cost effective escapement estimates for Chinook and coho salmon and steelhead.

Development and application of a technique to distinguish between coho salmon (Oncorhynchus kitsch) and steelhead (Oncorhynchus mykiss) redds and estimate adult populations from spawning surveys in several coastal Mendocino, County, California streams

Sun, 16 Apr 2023 12:28:11 -0700

Coastal salmon escapement monitoring - Spawning surveys were conducted in seven coastal Mendocino County streams between December 2001 and April 2002 to quantitatively estimate steelhead (Oncorhynchus mykiss) and coho salmon (O. kisutch) populations. Live adult, carcass, and redd areas were used to estimate adult populations using mark-recapture, area-under-the-curve (AUC), and redd area methods. Physical characteristics of positively identified coho salmon and steelhead redds were measured in detail and data analyzed using logistic regression to develop a discriminant function that identified redds to species. Information on spawning locations and distributions were collected. A stratified random block transect sampling design was used to estimate total populations from redd based methods and compared to total estimates. The discriminant function reduced uncertainty in redd identification from 18.4 to 3.9% and was used to differentiate between coho salmon, steelhead, unknown, and test redds when fish were not observed. Steelhead and coho salmon redds were significantly different in redd area and date of spawning. The average size of 331 steelhead redds was 1.51 m2 (S.E. = 0.49) and ranged from 0.3 to 6.66 m2. The average size of 261 coho salmon redds was 5.25 m2 (S.E. = 0.22) and ranged from 0.69 to 16.37 m2. Steelhead redd density was not significantly different among streams during 2001-02. Coho redd density was not significantly different among streams during 2001-02. Suggesting that these populations are behaving similarly within this geographic area thus may not be independent populations. Steelhead AUC and redd area population estimates are presented for three and six streams, respectively. Coho salmon population estimates from AUC, carcass mark-recapture, and redd area are reported for six coastal Mendocino County streams. AUC population estimates were similar to redd area estimates for coho salmon and steelhead. Steelhead fork lengths were not different among streams during 2001-02. Coho salmon fork lengths were not different among streams during 2001-02. Steelhead female to male ratio varied slightly among steams. Coho salmon female to male ratio was also varied slightly among streams. There was a large overlap in the timing of coho and steelhead spawning. Stratified random block transect sampling population estimates were not significantly different from redd area population estimates and will decrease field effort in the future. The discriminant function is robust for differentiating between Coho salmon and Steelhead based on physical redd characteristics and may be useful in other rivers where these species co-occur. Future work should employ stratified random block sampling, collect data on redds, carcasses, and adults, and calculate population estimates by redd area.

Bullfrog Predation on a Juvenile Coho Salmon in Humboldt County, California

Sun, 16 Apr 2023 12:27:49 -0700

coho salmon predation - Non-native bullfrogs eat native juvenile coho

Use of Historically Fishless High-Mountain Lakes and Streams By Nearctic River Otters (Lontra canadensis) in California

Sun, 16 Apr 2023 12:27:47 -0700

River otters in high-elevation habitats in California - In California, River Otters (Lontra canadensis) are most commonly associated with food-rich lowland aquatic habitats where they forage primarily on fish and crustaceans. Their distribution in high-elevation montane regions of the state, areas in which fish and crayfish were absent historically, is largely unknown. We compiled occurrence records of River Otters in California from elevations >1100 m, and evaluated them using evidentiary standards. Based on 126 records, we report the widespread presence of River Otters in the Klamath, southern Cascades, and Sierra Nevada mountain ranges, including at elevations exceeding 3000 m. Sixty-three percent of the records met our definition as “verified”, and the remaining 37% were considered “unverified”. The distribution of observations through time and habitats in which observations were made were similar between verified and unverified records. River Otter records spanned the period from 1900 to 2010, with 50% occurring between 1991 and 2010. Ninety-three percent of the water bodies with records of River Otters contained nonnative prey (fish and crayfish). Those lacking nonnative prey all supported native prey, including amphibians and reptiles. Based on records that contained River Otter foraging observations, nonnative fishes and crayfish were represented in 89% of the total accounts, and native frogs and invertebrates were represented in 22%. It remains unclear whether River Otters occurred in California's high-elevation water bodies prior to the introduction of fish and crayfish, and additional research is needed to understand the possible influence of nonnative prey in allowing River Otters to expand their distribution in these habitats.

Juvenile Salmonid Inventory of Baldface Creek, North Fork Smith River Basin, Oregon

Sun, 16 Apr 2023 12:27:44 -0700

coho salmon presence in Baldface Creek, Northfork Smith River - Results from a snorkel survey that occurred in a reach of baldface creek, northfork smith ricer, Oregon during the summer of 2013.

Supporting evidence in defining historic and recent occurrence of Coho Salmon (Oncorhynchus kisutch) in California streams within the Southern Oregon/ Northern California Evolutionary Significant Unit

Sun, 16 Apr 2023 12:21:42 -0700

Historic and Current SONCC Coho Distribution - This document provides the supporting evidence for the report: "Historic and recent occurrence of coho salmon (Oncorhynchus kisutch) in California streams within the Southern Oregon/ Northern California Evolutionarily Significant Unit. California Department of Fish and Game, Arcata, CA 78 p." The report can be found in the document library. This document establishes coho salmon presence in individual streams (by year) and traces this presence back to the original citation.

Natural resources of Lake Earl and the Smith River delta

Sun, 16 Apr 2023 12:09:02 -0700

Recommendations for preservation, maintenance and use of natural resources - Documentation of the natural resources of Lake Earl and the Smith River delta. Outline, evaluate problems and conflicts of use affecting resources and recommendations of Fish and Game for measures to protect and enhance the lake, delta and its environs.

Natural resources of the Eel River delta

Sun, 16 Apr 2023 12:08:58 -0700

Recommendations for preservation, maintenance and use of natural resources - Purpose of this report is to document the natural resources of the Eel River Delta, Humboldt County; outline, evaluate problems and conflicts of use affecting resources and recommendation of measures to protect and enhance the Delta and its environs.

The natural resources of Humboldt Bay

Sun, 16 Apr 2023 12:08:53 -0700

Recommendations for preservation, maintenance and use of natural resources - Fish and game's recommendations for preservation, maintenance and wise use of Humboldt Bay's natural resources.

Coastal Mendocino County salmonid life cycle and regional monitoring: monitoring status and trends for 2011

Sun, 16 Apr 2023 11:47:22 -0700

Coastal salmon escapement and life cycle monitoring - California’s coastal salmon and steelhead populations are listed under California and Federal Endangered Species Acts; both require monitoring to provide measures of recovery. Since 2004 the California Department of Fish and Game and NOAA Fisheries have been developing a monitoring plan for California’s coastal salmonids (the California Coastal Salmonid Monitoring Plan- CMP). The CMP will monitor the status and trends of salmonids at evolutionarily significant regional scales and provide population level estimates. For the CMP, data to evaluate adult populations are collected using a spatially balanced probabilistic design (e.g. Generalized Random Tesselation Stratified- GRTS). Under this scheme a two-stage approach is used to estimate status. Regional redd surveys (stage 1) are conducted in stream reaches in a GRTS sampling design at a survey level of 15% or = 41 reaches, which ever results in fewer reaches, of available habitat each year. Spawner: redd ratios are derived from smaller scale census watersheds (stage 2) where “true” escapement is estimated using capture-recapture methods. These are used to estimate regional escapement from expanded redd counts. In 2008-09 we applied the results of our previous studies to estimate salmonid escapement for the Mendocino coast region, the first implementation of the CMP in the state. Here we present the results of the first three years (2008-09 to 2010-11) of this monitoring effort and discuss our findings in context of expanding the CMP to all of coastal California. We discuss sample frame development, sample size, and present escapement data for major portions of the California Coastal Chinook Salmon Evolutionarily Significant Unit (ESU), the Central California Coho Salmon ESU, and the Northern California coastal Steelhead ESU. In addition, we present 2010-11 data from three life cycle monitoring streams and combine this information with previous years’ data to evaluate status and trends for coho and steelhead.

COASTAL MENDOCINO COUNTY SALMONID LIFE CYCLE AND REGIONAL MONITORING: MONITORING STATUS AND TRENDS 2010 2009-10 Final Report

Sun, 16 Apr 2023 11:29:22 -0700

regional salmonid monitoring CMP - This report documents the results of the second year of a multi-year regional salmonid monitoring program implemented as part of the California’s Coastal Salmonid Monitoring Program (CMP). This project was funded by the Fisheries Restoration Grants Program. The purpose of this study was to 1) continue salmon life cycle monitoring (adults in- smolts out) in three life cycle monitoring streams (LCS) and provide spawner: redd ratios for calibrating regional redd survey data to regional fish abundance estimates and, 2) conduct regional spawning ground surveys throughout coastal Mendocino County streams to estimate escapement and assess sampling rates at this regional scale.

Results of the 2000 Steelhead (Oncorhynchus mykiss) Fyke Trapping and Stream Resident Population Estimations and Predictions for the Noyo River, California with Comparison to Some Historic Information

Sun, 16 Apr 2023 11:26:19 -0700

smolt and juvenile salmon abundance - Downstream movement fyke trapping and over-summer resident population studies in the Noyo River were conducted during spring and summer 2000 to estimate juvenile and young-of-the-year (YOY) steelhead (Oncorhynchus mykiss) and coho (Oncorhynchus kisutch) population abundance, size, age, survival, migration timing, and distribution. Information was collected on all species found in the river and a simple population model was developed to predict YOY steelhead populations based on adult female estimates from spawning surveys. Juvenile habitat quality from historic stream surveys was compared to habitat use during 2000. Migrating steelhead population estimates ranged from 41,821 (95% CI = 6,126) for the summation of individual traps to 61,977 (95% CI = 13,241) for the two trap method. Coho population estimates ranged from 976 (95% CI = 1,407) for the two trap method to 3,812 (95% CI = 1,814) for the summation of individual traps. The summation of individual traps and the two trap population estimates were not significantly different (t = 0.11, p = 0.91, n = 5).

Results of the Winter 2000 Steelhead (Oncorhynchus mykiss) Spawning Survey on the Noyo River, California with Comparison to Some Historic Habitat Information

Sun, 16 Apr 2023 11:26:06 -0700

salmonid monitoring and escapment - Results of the Winter 2000 Steelhead (Oncorhynchus mykiss) Spawning Survey on the Noyo River, California with Comparison to Some Historic Habitat Information

Steelhead (Oncorhynchus mykiss) and Coho Salmon (Oncorhynchus kisutch) Juvenile Population Estimations and Predictions in the Noyo River, California Spring and Summer 2001

Sun, 16 Apr 2023 11:25:56 -0700

smolt and juvenile salmon abundance - Modified fyke/pipe trapping and April-June resident population studies in the Noyo River were conducted during spring and summer 2001 to estimate juvenile and young-of-the-year (YOY) steelhead (Oncorhynchus mykiss) and coho (Oncorhynchus kisutch) population abundance, size, age, survival, migration timing, and distribution. Information was collected on all species captured and a simple population model was used to predict YOY steelhead populations based on adult female estimates from spawning surveys. Steelhead population estimates ranged from 73,114 (SD = 29,446) for the summation of individual traps to 290,059 (SD = 69,574) for the two-trap method. Coho population estimates ranged from 26,756 (SD = 5,229) for the two-trap method to 25,029 (SD = 6,121) for the summation of individual traps.

Results of the 2000-2001 Coho Salmon (Oncorhynchus kisutch) and Steelhead (Oncorhynchus mykiss) spawning surveys on the Noyo River, California

Sun, 16 Apr 2023 11:25:53 -0700

steelhead monitoring - Spawning surveys were conducted in the Noyo River between December 2000 and April 2001 to quantitatively estimate steelhead (Oncorhynchus mykiss) and coho salmon (O. kisutch) populations. Adult, carcass, redd counts, and redd areas were used to estimate adult populations using the area-under-the-curve (AUC) and two redd-based methods. Physical characteristics of coho salmon and steelhead redds were measured in detail and data analyzed using principle components analysis (PCA) to develop a linear discriminant function that identified redds to species. Information on spawning locations and distributions were collected. Redd based steelhead population estimates ranged from 258 (± 7) to 583 (± 16) and the AUC estimate was 222 (95% CI 127-416). The redd based coho salmon population estimate was 555 (± 16) and the AUC estimate was 592.

Juvenile salmonid (Oncorhynchus kisutch, O. mykiss, and O. tshawytscha) abundance estimation in the upper Noyo River, California during spring and summer 2002

Sun, 16 Apr 2023 11:22:20 -0700

smolt and juvenile salmon abundance - Modified fyke/pipe trapping and April-June resident population studies in the upper Noyo River were conducted during spring and summer 2002 to estimate juvenile and young-of-the-year (YOY) steelhead (Oncorhynchus mykiss) and Chinook (O. tshawytscha) and coho salmon (O. kisutch) population abundance, size, age, survival, migration timing, and distribution. Information was collected on all species captured and data was compared to results from 2000 and 2001. Six traps were placed in the Noyo River in late-March 2002 and checked daily until 20 June 2002. All steelhead, coho, and chinook salmon >50 mm were marked with weekly and trap-specific freeze brands. Fish < 50 mm fork length were counted. Marked fish were released above traps and recaptured fish were released below the traps. Modified fyke/pipe population estimates were computed using a maximum-likely-hood estimate for stratified populations. Populations were estimated by summing all trap estimates and using a two-trap markrecapture method. One hundred meter reaches above and below each trap site were electro-fished a minimum of four times between April and July. All steelhead and coho >50 mm were marked with site and time specific freeze brands and released. Fish < 50 mm were counted and released. Resident population estimates were computed using the Jolly-Seber method for each reach and expanded to estimate stream resident populations. Steelhead and coho populations were estimated for traps and stream reaches and survival estimates were made. Steelhead trap population estimates were not different among years. Coho YOY trap population estimates were and Y+ were not significantly different among years. Capture probabilities were not significantly different between steelhead and coho salmon > 50 mm (t = -0.76, p = 0.46, n = 5) during 2002. Rearing population estimates for stream segments were not different between years. Steelhead and Coho survival estimates were not different from estimates reported in the literature. Downstream movement and resident population monitoring could continue in the upper Noyo River to follow cohorts through successive life stages, although the 2002 results suggest the use of trapping for long term monitoring should be approached cautiously.

Do young coho salmon and steelhead spring emigration abundance estimates or summer density and rearing estimates reflect the status or trends of adult populations?

Sun, 16 Apr 2023 11:22:18 -0700

salmonid smolt juvenile and adult data relations - There is a need for reliable estimates of threatened adult coho salmon and steelhead abundance in coastal Northern California. However, most monitoring programs in this area are focused on juvenile emigration in spring or summer rearing. Thus it is important to understand the relationship between adult escapement and juvenile abundance. We used four consecutive years data on adult female coho salmon and steelhead escapement, young-of-the-year (YOY) and older age fish abundance estimates from down stream trapping studies, and YOY and juvenile rearing population indices in several coastal streams in Northern California to evaluate if YOY and juvenile trapping programs operated annually from March to June and summer rearing density estimates were correlated with adult escapement (status). We examined these data to determine if YOY and juvenile abundance trends track those of adult populations. Trends were examined by comparing the slopes of adult versus year and juvenile abundance versus year, treating sites as samples, with paired t-tests. Steelhead YOY and coho salmon YOY and yearlings (Y+) trapping population estimates and adult female escapement were significantly correlated (r >0.52, p < 0.02). Older age steelhead trapping abundance and adult female escapement were not significantly related (r < 0.17, p > 0.44). Adult female escapement and summer rearing densities were not significantly related for either species (r < 0.004 p > 0.49). Steelhead YOY summer rearing populations were significantly related to adult female escapement (r = 0.41 p = 0.02) but coho YOY and older age steelhead were not (r > 0.05, p > 0.21). YOY and Y+ coho salmon trapping abundance were significantly related to adult returns in subsequent years (r > 0.42, p < 0.03). With four years data, trends in adult abundance were not significantly different than YOY and older age fish trends for summer rearing and emigrant abundance estimates (t < 1.44, p> 0.21). However, these trends were not significantly different than zero (t < 0.96 p > 0.08). Our results suggest that downstream emigrant trapping of YOY steelhead and YOY and Y+ coho were reliable indices of adult abundance. Summer rearing density and population estimates based on electro-fishing were not reliable indices of adult escapement and monitoring programs employing this approach should be undertaken with caution. Summer rearing and downstream emigrant trapping may be reasonable tools for long term trend detection of adult populations. More years’ data will be required to fully understand the relationship between these metrics.

Juvenile salmonid (Oncorhynchus kisutch, O. mykiss, and O. tshawytscha) abundance estimation in the upper Noyo River, California spring 2003

Sun, 16 Apr 2023 11:22:17 -0700

smolt and juvenile salmon abundance - Modified fyke/pipe trapping and April-June resident population studies in the upper Noyo River were conducted during spring and summer 2003 to estimate juvenile and young-of-the-year (YOY) steelhead (Oncorhynchus mykiss) and Chinook (O. tshawytscha) and coho salmon (O. kisutch) population abundance, size, age, survival, migration timing, and distribution. Information was collected on all species captured and data was compared to results from 2000, 2001, and 2002. Six traps were placed in the Noyo River in late-March 2003 and checked daily until 22 June 2003. All steelhead, coho, and chinook salmon >50 mm were marked with weekly and trap-specific freeze brands. Fish < 50 mm fork length were counted. Marked fish were released above traps and recaptured fish were released below the traps. Modified fyke/pipe population estimates were computed using a maximum-likely-hood estimate for stratified populations. Populations were estimated by summing all trap estimates and using a two-trap mark-recapture method. One hundred meter reaches above and below each trap site were electro-fished a minimum of four times between April and July. All steelhead and coho >50 mm were marked with site and time specific freeze brands and released. Fish < 50 mm were counted and released. Resident population estimates were computed using the Jolly-Seber method for each reach and expanded to estimate stream resident populations. Steelhead and coho populations were estimated for traps and stream reaches and survival estimates were made. Steelhead trap population estimates were different among years. Coho YOY trap population estimates were and Y+ were not significantly different among years. Rearing density estimates for stream segments were not different between years. Steelhead and coho survival estimates were not different from estimates reported in the literature. Downstream movement and resident population monitoring could continue in the upper Noyo River to follow cohorts through successive life stages, although the 2003 results suggest the use of trapping for long term monitoring should be approached cautiously.

Annual coho salmon (Oncorhynchus kisutch) and steelhead (O. mykiss) spawning ground escapement estimates 2000 to 2004 in several coastal Mendocino County, California streams and recommendations for long term monitoring of coastal salmonids

Sun, 16 Apr 2023 11:22:15 -0700

Coastal salmon escapement monitoring - I estimated escapement from spawning ground surveys in Caspar and Pudding (PC) creeks and the South Fork Noyo (SF) and Little rivers during 2003-04 using redd data and the area-under-the-curve. Coho salmon and steelhead were tagged entering PC and recaptured during spawning surveys to estimate abundance. Known numbers of coho salmon were tagged and released above the SF Egg Collecting Station (ECS). Coho salmon carcasses capture-recapture was used to estimate escapement for all four streams. Recoveries of tagged fish in PC and the SF were used to estimate residence time (rt) and observer efficiency (e) and compared to other estimates of these values. Including 2001, 2002, and 2003 escapement estimates for these streams, capture-recapture estimates were not different than other methods except assuming one redd per female and redd counts and escapement were correlated. Estimates of the number of coho salmon per redd were different in PC and the SF in 2003-04, but the 2000 to 2004 SF average was not different than the 2003-04 PC estimate and escapement estimated from these values were not significantly different. The 2000 to 2003 average number of steelhead per redd in the Noyo River was not different than the 2003-04 PC estimate and escapement estimated using these values were not significantly different. These results indicate that estimates of the number of fish per redd can be transferred among steams to estimate populations from redd counts. Estimates of rt and e were variable, depended on estimation method, were not different for coho salmon between PC and the SF, and may be transferable among streams. Coho salmon abundance over four years and for one complete life cycle (2000 to 2004) did not show clear trends. The purpose of this study was to 1) produce annual estimates of coho salmon and steelhead escapement from spawning ground surveys in four coastal Mendocino County streams, 2) continue to evaluate sources of bias in spawning ground escapement estimates (redd based, AUC, and carcass capture-recapture) and compare these to capture-recapture escapement estimates of coho salmon and steelhead in PC and coho salmon releases above the ECS, 3) evaluate trends in adult coho salmon escapement 2000 to 2004, and 4) provide recommendations for long-term regional monitoring of California’s coastal salmonids.

Evaluation of coho salmon (Oncorhynchus kisutch) and steelhead (O. mykiss) spawning ground escapement estimates for monitoring status and trends of California coastal salmonids: 2000 to 2005 escapement estimates for several Mendocino County, coastal streams

Sun, 16 Apr 2023 11:22:13 -0700

Coastal salmon escapement monitoring - I estimated escapement from spawning ground surveys in Caspar and Pudding (PC) creeks and the South Fork Noyo (SF) and Little rivers during 2004-05 using redd data and the Area-Under-the-Curve. Coho salmon and steelhead were tagged entering PC and recaptured during spawning surveys to estimate abundance. Known numbers of coho salmon were tagged and released above the SF Egg Collecting Station (ECS). Coho salmon escapement was estimated with carcass capture-recapture in all four streams. Recoveries of tagged fish in PC and the SF were used to estimate residence time (rt) and observer efficiency (e) and compared to other estimates of these values. Including 2001 to 2004 escapement estimates for these streams, capture-recapture estimates and redd counts were significantly correlated and equally reliable for monitoring escapement. Only escapement estimates assuming one redd per female were significantly different than estimates from other methods. Estimates of the number of coho salmon and steelhead per redd were not different among streams and years and escapement estimated using these values were not significantly different. Results indicated that estimates of the number of fish per redd can be transferred among steams to estimate populations from redd counts and that these estimates are equally reliable compared to capture-recapture or total counts. Carcass capture-recapture did not work for steelhead and may not be appropriate for long term regional monitoring. Estimates of rt and e were variable, depended on estimation method, were not different among streams and years, and may be transferable among streams. Coho salmon abundance over five years and for two complete life cycles did not show clear trends. The purpose of this study was to 1) determine the most reliable method of estimating spawning ground survey based salmonid escapement for status and trend monitoring, 2) produce annual escapement estimates for several coastal Mendocino County streams 2000 to 2005, 3) evaluate trends in abundance, and 4) provide recommendations for monitoring coastal salmon populations.

A regional approach to monitoring salmonid abundance trends: A pilot project for the application of the California Coastal Salmonid Monitoring Plan in coastal Mendocino County year 1

Sun, 16 Apr 2023 11:22:11 -0700

Coastal salmon escapement monitoring - This report documents the first year results of a three-year pilot, funded by the Fisheries Restoration Grants Program, to evaluate salmonid monitoring methodologies for California’s Coastal Monitoring Plan (CSMP). We considered five coastal Mendocino County streams as a hypothetical region of California to evaluate the use of life cycle monitoring streams (LCS) and regional spawning surveys (SGS) for monitoring salmonids at a regional scale. The primary purpose of this study was to assess: 1) if the field sampling protocols provided statistically valid and accurate estimates, 2) the logistical problems encountered, and 3) the level of resources needed for regional LCS and SGS monitoring. We examined escapement estimation methods, calibration of SGS data from LCS data, regional sampling rates, and produced annual abundance estimates and evaluated regional trends. To estimate LCS escapement and calibrate potential bias in SGS estimates we used live fish capture-recapture methods. Fish were captured and tagged at the Pudding Creek fish ladder, the Noyo River Egg Collecting Station (ECS), and a floating board resistance weir in Caspar Creek. Recaptures were visual observations of fish during SGS in these streams. For regional SGS escapement estimates two sampling designs were used: 1) SGS conducted in three streams at 33% sampling and resulting stream estimates summed with LCS estimates to calculate regional escapement (33% sum of streams), and 2) SGS conducted in a Generalized Random Tessellation Sampling (GRTS) frame draw at 10%. All habitat in each LCS was surveyed providing a systematic sample of 37 (48%) additional reaches to examine regional sampling rate. To estimate SGS escapement we used carcass capture-recapture, live fish counts, redd counts, redd area measurements, and spawner: redd ratios developed in the LCS. The LCS capture-recapture methods produced reliable coho escapement estimates for Pudding Creek and the South Fork Noyo River and provided information for reducing bias in SGS estimates. Carcass capture-recapture was not reliable because too few carcasses were observed. Regional SGS escapement was best estimated using spawner: redd ratios developed at LCS streams. The 10% and 48% GRTS escapement estimates overlapped the 33% sum of stream estimates but the variance was higher at 10%. Redd area escapement estimates were not different from capture-recapture estimates for steelhead, but were for coho due to difficulties counting coho redds experienced during 2005-06. We recommend annual evaluation of the relationship between redd counts; redd based escapement estimates, and capture-recapture estimates to determine the best method for estimating abundance from SGS data. For regional monitoring the annual GRTS sample draw should be increased to = 24 reaches to evaluate sampling rates between 10% and 30% and account for access issues.

A regional approach to monitoring salmonid abundance trends: A pilot project for the application of the California Coastal Salmonid Monitoring Plan in coastal Mendocino County Year II

Sun, 16 Apr 2023 11:22:06 -0700

Coastal salmon escapement monitoring - We considered five coastal Mendocino County streams as a hypothetical region of California to evaluate the use of life cycle monitoring streams (LCS) and regional ground spawning surveys (SGS) for monitoring salmonid populations at a regional scale. The primary purpose of this study was to assess: 1) if the field sampling protocols provided statistically valid and accurate estimates, 2) the logistical problems encountered, and 3) the level of resources needed for regional LCS and SGS monitoring. We examined escapement estimation methods, calibration of SGS data from LCS data, regional sampling rates, produced annual abundance estimates, and evaluated regional trends. To estimate LCS escapement and calibrate potential bias in SGS estimates we used live fish capture-recapture methods. Fish were captured and tagged at the Pudding Creek fish ladder, the Noyo River Egg Collecting Station (ECS), and a floating board resistance weir in Caspar Creek. Recaptures were visual observations of fish during SGS in these streams. For regional SGS escapement estimates two sampling designs were used: 1) SGS conducted in three streams at 33% sampling and resulting stream estimates summed with LCS estimates to calculate regional escapement (Sum of Streams-SOS), and 2) SGS conducted in a Generalized Random Tessellation Sampling (GRTS) frame draw at 10%. All habitat in each LCS was surveyed providing a systematic sample of 29 additional reaches to examine regional sampling rate. Additional reaches were selected in GRTS order to evaluate results of sampling at 10%-35% GRTS. To estimate adult escapement in spawning reaches we used carcass capture-recapture, live fish counts, redd counts, redd area measurements, and spawner: redd ratios developed in the LCS. The LCS capture-recapture methods produced reliable coho escapement estimates for Pudding Creek and the South Fork Noyo River and provided information for reducing bias in SGS estimates. Carcass capture-recapture was not reliable because too few carcasses were observed. Regional SGS escapement was best-estimated using spawner: redd ratios developed at LCS streams. The 10% GRTS escapement estimates were not different from the SOS estimates and precision was within 30%. Increasing GRTS sampling effort did not improve the escapement estimates or their precision. Exploration of regional coast-wide sample size needs based on data collected for this study suggest sample sizes will be much smaller (thus less expensive) than previously anticipated. We recommend annual evaluation of spawner: redd ratio conversions of redd counts into escapement relative to capture-recapture escapement estimates as the best approach for estimating abundance for regional spawning ground surveys.

A regional approach to monitoring salmonid abundance trends: A pilot project for the application of the California Coastal Salmonid Monitoring Plan in coastal Mendocino County Year III

Sun, 16 Apr 2023 11:22:04 -0700

Coastal salmon escapement monitoring - We treated five coastal Mendocino County streams as a coastal region of California to evaluate the use of life cycle monitoring streams (LCS) and regional spawning surveys (SGS) for monitoring salmonid population escapement. The primary purpose of this study was to assess: 1) if the field sampling protocols provided statistically valid and accurate adult abundance estimates, 2) the logistical problems encountered, and 3) the level of resources needed for regional LCS and SGS monitoring. We examined escapement estimation methods, calibration of SGS data from LCS data, regional sampling rates and statistical power, produced annual abundance estimates, and evaluated regional trends. To estimate LCS escapement and calibrate potential bias in SGS estimates we used live fish capture-recapture methods and spawning ground surveys in three LCS. Fish were captured and tagged at the Pudding Creek fish ladder, the Noyo River Egg Collecting Station (ECS), and a floating board resistance weir in Caspar Creek. Recaptures were visual observations of fish during SGS in these streams. Redds were counted in all reaches in the three LCS. To estimate regional escapement, spawning density was estimated in a random sample of stream reaches and expanded to calculate total regional escapement. For regional SGS escapement estimates two sampling designs were used: 1) a 10% sampling rate of stream reaches in our regional area drawn by a Generalized Random Tessellation Sampling (GRTS) scheme, and 2) a 33% stream reach sampling rate in non-LCS combined with total count estimates from LCS for a Sum-of-Streams (SOS) regional estimate. Additional reaches were selected in GRTS order to evaluate results of sampling at 10%-35% GRTS during the last two years of study. To estimate adult escapement in spawning reaches we used carcass capture-recapture, live fish counts, redd counts, redd area measurements, and spawner: redd ratios developed in the LCS. We evaluated sample size and statistical power for application of this approach to regional escapement monitoring. The LCS capture-recapture methods produced reliable coho escapement estimates for Pudding Creek and the South Fork Noyo River and provided information for reducing bias in SGS estimates. The coho and steelhead capture-recapture estimates for the other LCS streams had large confidence bounds due to the low numbers of marked and recaptured fish. Carcass capture-recapture was not reliable because too few carcasses were observed. Regional SGS escapement was best-estimated using spawner: redd ratios developed at LCS streams. The 10% GRTS escapement estimates were not different from the SOS estimates and precision was within 30%. Increasing GRTS sampling effort did not improve the escapement estimates or their precision. The results of this study suggest that a sample size of = 40 reaches should have sufficient statistical power to detect regional trends in salmon populations.

Weir Mark-Recapture/Resight Protocols

Wed, 28 Sep 2022 14:21:55 -0700

salmon mark recapture protcols - This protocol is designed for both temporary and permanent types of weir monitoring programs. The goal of this program is to implement a successful mark-recapture and/or resight program to accurately estimate the number of returning adult salmonids.

Coastal Northern California Salmonid Spawning Survey Protocol

Wed, 28 Sep 2022 14:20:06 -0700

Salmon Spawning Survey Protocols - The purpose of this Protocol is to describe field methods for collecting information to estimate salmonid escapement in coastal Northern California streams. Predetermined, 2-3 km reaches (See Boydstun and MacDonald 2005for discussion of the rotating panel design and reach selection process) will be surveyed biweekly (Gallagher and Gallagher 2005) beginning in late-November, with one survey occurring prior to fish entering spawning areas, and continuing until late-April (or when new redds and fish are no longer observed). Each reach should be surveyed a maximum of two weeks apart and stream flows and/or weather conditions will have some bearing on the temporal intensity of surveys. All redds will be identified to species, measured, and geo-referenced. All live and dead fish will be identified, inspected for tags, measured, and untagged carcasses will be marked. Redd longevity and observer efficiency in redd detection should be estimated for each watershed each year following Gallagher and Gallagher (2005). The condition of redds measured during previous surveys will be recorded to assess the duration of redd observability and observer efficiency.

Smith River Plain Dissolved Copper Monitoring Report 2017-2018

Fri, 04 Dec 2020 14:21:02 -0800

Water Quality - Results from the fall 2017 and spring 2018 dissolved copper sampling effort verify the results found with the NCRWQCB’s 2013-2015 sampling effort, which point to agriculture, and specifically, lily bulb farming as a significant source of the dissolved copper observed in the tributaries of the Smith River Plain. The levels observed at times exceeded the levels where sublethal, neurobehavioral effects would be expected to occur in juvenile life stages of coho salmon and likely would exceed criteria calculated through EPA’s biotic ligand model methodology. Neither hardness nor DOC appear to be at levels that significantly reduce the toxicity of copper to coho salmon. While DOC was only available for the spring 2018 samples for our study, we reviewed NCRWQCB’s water quality data for the area since 2011 and confirmed that Delilah, Rowdy and Morrison creeks had DOC concentrations below 6 mg/L. Sites located above lily bulb fields consistently showed dissolved copper greater than zero, indicating that a possible source of copper other than that used as fungicide factors in to the levels measured. Interestingly, most of the sites upstream of the lily bulb fields had lower copper concentrations during the spring sampling event compared to the fall one. This could be because pesticide spraying may have not coincided as closely with the spring sampling event as with the fall one or copper accumulations over the dry periods may have resulted in higher levels of copper run-off during the fall.

Off-Site Biological Monitoring of Anadromous Salmonid Populations in the Mad River in 2017.18: Fullfillment of annual Requirements for Mad River Hatchery's Hatchery and Genetic Management Plan

Tue, 16 Jun 2020 15:55:04 -0700

Sonar monitoring - Sonar monitoring for compliance for the MRH HGMP

Sonar Estimation of California Coastal Chinook Salmon, NC Fall Run Steelhead, SONCC Coho Salmon, and Pink Salmon in Mad River 2017

Tue, 16 Jun 2020 15:54:49 -0700

Sonar monitoring - Sonar Monitoring for HGMP compliance.

Results of regional spawning ground surveys and estimates of total salmonid redd abundance in the South Fork Eel River, Humboldt and Mendocino Counties California, 2018-2019

Tue, 07 May 2019 11:07:45 -0700

regional salmonid monitoring CMP - The 2018-19 South Fork Eel River Adult Salmonid Redd Abundance Monitoring Project conducted 232 spawning ground surveys upon 38 spatially balanced and randomly selected sample reaches in the South Fork Eel River watershed between November 5, 2018 and, February 11, 2019. Each sample reach was surveyed an average of 4.9 times, and the average interval between surveys for all reaches was 19.9 days. The 2018-2019 survey observed 41 live coho salmon, 42 live Chinook salmon, 18 live steelhead,18 unidentified live salmonids, 4 coho salmon carcasses, and 10 Chinook salmon carcasses. A total of 246 redds were detected, and 15 of those redds were observed to be associated with a specific salmonid species digging or guarding the redd. The remaining 231 redds were assigned a species using a k-Nearest Neighbors algorithm analysis. The number of redds observed in the 38 sample reaches was expanded to estimate the number of redds constructed across the entire South Fork Eel River reach sample frame. Redd abundance estimates for the 2018-2019 spawning season in the South Fork Eel River sample frame area, including 95% confidence intervals, are: 990 (205, 1776) coho salmon redds, 404 (131, 676) Chinook salmon redds*, and 322 (168, 476)steelhead redds

A Survey of Aquatic Habitats, Fishes and other Aquatic Fauna of Elk Creek, Crescent City, California

Wed, 16 Jan 2019 12:51:29 -0800

Fisheries and other Aquatic Fauna Inventory - I initiated this study in 2013 to determine current occupancy status and spatial distributions of salmonids, among other species, occurring in Elk Creek. This study should provide landowners, managers, and restoration groups better information on the aquatic species occurring in Elk Creek while identifying remaining information gaps. I used opportunistic field sampling focused on determining Coho Salmon, among other salmonids, presence annually from 2013 to 2018. In addition, I conducted a literature review focused on aquatic vertebrates of Elk Creek to determine what vertebrate aquatic fauna have been described using Elk Creek in the past. Collectively, these results will help inform future monitoring and management of this unique and biologically important watershed.

Rapid assessment of salmonid habitat protocol

Tue, 18 Sep 2018 11:37:46 -0700

Salmonid habitat monitoring - The goal of the Regional Salmonid Habitat Monitoring effort is to estimate the volume of preferred habitatavailable to juvenile salmonids in six watersheds in coastal Mendocino County. We will estimate the total area and volume of stream habitat available in all survey reaches, as well as. At the end of the season we will apply the values from the Caspar/Pudding Creek suitability curves to the volume estimates in order to provide an idea of how much preferred habitat volume is available to juvenile salmonids. Eventually, with more crew resources we hope to strengthen our fish-habitat preference suitability curves with more observations, in order to provide fishery managers and restoration practitioners with the best information possible to guide restoration efforts.

Juvenile Salmonid Use and Restoration Assessment of the Tidal Portions of Selected Tributaries to Humboldt Bay, California, 2011-2012

Mon, 16 Jul 2018 12:21:05 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - California Department of Fish and Wildlife and Pacific States Marine Fisheries Commission staff sampled the stream-estuary ecotone of selected Humboldt Bay tributaries to document their use by juvenile salmonids and to assess estuarine habitat restoration projects. We sampled fish using seine nets and minnow traps baited with frozen salmon roe. Juvenile coho salmon (Oncorhynchus kisutch) was the most numerous salmonid captured but we also commonly captured Chinook salmon (O. tshawytscha), steelhead trout (O. mykiss), and cutthroat trout (O.clarkii clarkii). Sub yearling coho salmon were present from April to December with peak catches occurring in the summer. Their mean ecotone residence time was one to two months but individual fish reared there up to eight months. Age 1+ coho salmon were present during the winter and spring. One group of Age 1+ coho arrived in the ecotone in the fall and reared there throughout the winter and into the spring. A later group of Age 1+ coho emigrated through the ecotone relatively quickly primarily during May. Juvenile Chinook salmon were present only in Freshwater Creek Slough in the late spring and early summer. Juvenile steelhead trout and cutthroat trout were captured throughout the year and some reared for months in the ecotone. Mean growth rates of juvenile salmonids in the ecotone were typically 0.15 to 0.25 mm/day which was higher than growth rates observed by other projects in stream habitats upstream of the ecotone. Juvenile salmonids sought out freshwater rather than brackish water habitat while rearing in the ecotone. Juvenile salmonids, especially coho salmon, utilized newly constructed ponds as soon as they were completed and fall/winter stream flow converted the ponds to fresh water habitat. The stream-estuary ecotone provides productive rearing habitat for juvenile salmonids, especially over winter habitat for juvenile coho salmon.

Juvenile salmonid use of the tidal portions of selected tributaries to Humboldt Bay, California, 2013-2015

Mon, 16 Jul 2018 12:20:55 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - California Department of Fish and Wildlife and Pacific States Marine Fisheries Commission staff sampled the stream-estuary ecotone (SEE) of selected Humboldt Bay tributaries to document their use by juvenile salmonids and to assess estuarine habitat restoration projects. We sampled fish using seine nets and minnow traps baited with frozen salmon roe. Juvenile coho salmon (Oncorhynchus kisutch) was the most numerous salmonid captured but we also commonly captured Chinook salmon (O. tshawytscha), steelhead trout (O. mykiss), and cutthroat trout (O.clarkii clarkii). Subyearling coho salmon were present from April to December with peak catches occurring in the summer and fall. Their mean SEE residence time was one to two months but individual fish reared there for close to a year. Yearling-plus coho salmon were present primarily during the winter and spring. One group of Age 1+ coho arrived in the SEE in the fall and reared there throughout the winter and into the spring. A later group of Age 1+ coho emigrated through the SEE relatively quickly primarily during May. Juvenile Chinook salmon were present only in Freshwater Creek Slough in the late spring and early summer. Juvenile steelhead trout and cutthroat trout were captured throughout the year and some reared for months and possibly years in the SEE. Mean growth rates of juvenile salmonids in the ecotone were typically 0.15 to 0.25 mm/day which was higher than growth rates observed by other projects in stream habitats upstream of the SEE; however, juvenile salmonid growth rates in off channel ponds were usually higher. Juvenile salmonids sought out freshwater rather than brackish water habitat while rearing in the SEE. Juvenile salmonids, especially coho salmon, utilized newly constructed off channel ponds as soon as they were completed and fall/winter stream flow converted the ponds to fresh water habitat. Drought conditions from 2013 to 2015 affected SEE habitat in that higher water temperatures and salinities along with lower dissolved oxygen levels persisted for longer periods of time. Juvenile coho salmon delayed their fall arrival to the SEE, a higher than normal portion of yearling-plus coho salmon spent a second summer in SEE habitat, and juvenile salmonids were smaller and slower growing than most other years are all evidence that the drought altered juvenile salmonid behavior.

Sport Fish Restoration Annual Project Performance Report 2015

Mon, 16 Jul 2018 12:20:28 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the past year CA Dept. of Fish and Wildlife’s (CDFW) Natural Stocks Assessment Project (NSA) sampled the tidal portion of upper Freshwater Creek Slough, Wood Creek, Ryan Creek, Jacoby Creek, Martin Slough, and Salmon/Cattail Creek estuary to document their use by juvenile salmonids. NSA also assessed completed estuarine habitat restoration projects in Martin Slough and Wood and Salmon Creeks and pre-project conditions in Jacoby Creek by describing juvenile salmonid use and basic water quality conditions in these locations. Salmonid recovery plans encouraged numerous estuary and marsh habitat restoration projects around Humboldt Bay (NMFS 2012; HBWAC 2005; CDFG 2004). This project, by describing life history traits and habitat needs of juvenile salmonids in the stream estuary ecotone of Humboldt Bay, has already played an important role by providing needed data to help in the design local estuarine habitat restoration projects. NSA operated PIT tag antennas in Wood and Salmon Creeks to assess the performance of a newly constructed off channel ponds as over winter habitat for juvenile salmonids and operated a PIT tag antenna in Ryan Creek to better describe the use of the streamestuary ecotone by juvenile salmonids. NSA also participated on technical review teams to develop project criteria and review restoration project designs for planned projects in Freshwater Creek, Wood Creek, Jacoby Creek, and continuing projects on Salmon/Cattail Creeks. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout and by assessing the performance of newly constructed off channel ponds this project hopes to provide important data to the restoration community to help restoration planning projects succeed.

Sport Fish Restoration Annual Project Performance Report 2014

Mon, 16 Jul 2018 12:20:09 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the past year CA Dept of Fish and Wildlife’s (CDFW) Natural Stocks Assessment Project (NSA) continued to sample the tidal portion of upper Freshwater Creek Slough, Wood Creek, Ryan Creek, Jacoby Creek, and Salmon/Cattail Creek estuary to document their use by juvenile salmonids. NSA also assessed estuarine habitat restoration projects in Wood and Salmon Creeks and collected data to describe pre-project conditions in Jacoby Creek. Salmonid recovery plans encouraged numerous estuary and marsh habitat restoration projects around Humboldt Bay (NMFS 2012; HBWAC 2005; CDFG 2004). This project, by describing life history traits and habitat needs of juvenile salmonids in the stream-estuary ecotone of Humboldt Bay, has already played an important role by providing needed data to help in the design local estuarine habitat restoration projects. NSA monitored the effects of marsh restoration projects in Wood and Salmon Creeks on juvenile salmonid use and basic water quality conditions, specifically in the newly created off channel ponds. NSA installed PIT tag antennas in Wood and Salmon Creeks to assess the performance of a newly constructed off channel pond as over winter habitat for juvenile salmonids and installed a PIT tag antenna in Ryan Creek to better describe the use of the stream-estuary ecotone by juvenile salmonids. NSA continued pre-project monitoring of an off channel habitat restoration project in Jacoby Creek that will connect an existing isolated pond to Jacoby Creek. NSA also participated on technical review teams to develop project criteria and review restoration project designs for planned projects in Freshwater Creek, Wood Creek, Jacoby Creek, and continuing projects on Salmon/Cattail Creeks. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout and by assessing the performance of newly constructed off channel ponds this project hopes to provide important data to the restoration community to help restoration planning projects succeed. Planned habitat restoration projects were delayed in Martin Slough so we will begin to collect preproject data there in 2014-15.

Sport Fish Restoration Annual Project Performance Report 2013

Mon, 16 Jul 2018 12:20:00 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the past year CA Dept of Fish and Wildlife’s (CDFW) Natural Stocks Assessment Project (NSA) continued to sample the tidal portion of upper Freshwater Creek Slough, Wood Creek, Ryan Creek, and Salmon Creek estuary to document their use by juvenile salmonids and to assess estuarine habitat restoration projects in Wood and Salmon Creeks. Salmonid recovery plans encouraged numerous estuary and marsh habitat restoration projects around Humboldt Bay (NMFS 2012; HBWAC 2005; CDFG 2004). This project, by describing life history traits and habitat needs of juvenile salmonids in the stream-estuary ecotone of Humboldt Bay, has already played an important role by providing needed data to help in the design local estuarine habitat restoration projects. NSA monitored the effects of marsh restoration projects in Wood and Salmon Creeks on juvenile salmonid use and basic water quality conditions, specifically in the newly created off channel ponds. NSA installed PIT tag antennas in Wood and Salmon Creeks to assess the performance of a newly constructed off channel pond as over winter habitat for juvenile salmonids and installed a PIT tag antenna in Ryan Creek to better describe the use of the stream-estuary ecotone by juvenile salmonids. NSA began pre-project monitoring of an off channel habitat restoration project in Jacoby Creek October that will connect an existing isolated pond to Jacoby Creek sometime in 2014. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout and by assessing the performance of newly constructed off channel ponds this project hopes to provide important data to the restoration community to help restoration planning projects succeed. Planned habitat restoration projects were delayed until late summer 2013 in Martin Slough so we will begin to collect pre-project data there in late 2013 if the project begins.

Sport Fish Restoration Annual Project Performance Report 2012

Mon, 16 Jul 2018 12:19:49 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the past year CA Dept of Fish and Game’s (DFG) Natural Stocks Assessment Project (NSA) continued to sample the tidal portion of upper Freshwater Creek Slough, Wood Creek, Ryan Creek, and Salmon Creek estuary to document their use by juvenile salmonids and to assess estuarine habitat restoration projects in Wood and Salmon Creeks. Salmonid recovery plans encouraged numerous estuary and marsh habitat restoration projects around Humboldt Bay (HBWAC 2005; CDFG 2004). This project, by describing life history traits and habitat needs of juvenile salmonids in the stream-estuary ecotone of Humboldt Bay, has already played an important role by providing needed data to help in the design local estuarine habitat restoration projects. NSA monitored the effects of marsh restoration projects in Wood and Salmon Creeks on juvenile salmonid use and basic water quality conditions, specifically in the newly created off channel ponds. NSA installed PIT tag antennas in Wood and Salmon Creeks to assess the performance of a newly constructed off channel pond as over winter habitat for juvenile salmonids. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout and by assessing the performance of newly constructed off channel ponds this project hopes to provide important data to the restoration community to help restoration planning projects succeed. Planned habitat restoration projects were delayed until late summer 2013 in Martin Slough so we will begin to collect pre-project data there in 2013. We plan to begin pre-project sampling in Jacoby Creek October 2012.

Sport Fish Restoration Annual Project Performance Report 2011

Mon, 16 Jul 2018 12:19:40 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the duration of this contract period (2009-2011) NSA continued to sample the tidal portion of upper Freshwater Creek Slough, Wood Creek, and Salmon Creek estuary to document their use by juvenile salmonids. NSA completed sampling in lower Freshwater Creek Slough, Elk River Slough, Hookton Slough, Jacoby Creek, Gannon Slough, Martin Slough, and Rocky Gulch. NSA initiated sampling in Ryan Creek Slough to determine how juvenile salmonids use the Freshwater-Ryan stream-estuary ecotone as a rearing area. Finally, NSA installed PIT tag antennas in Wood Creek to assess the performance of a newly constructed off channel pond as over winter habitat for juvenile coho salmon. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout and by assessing the performance of newly constructed off channel ponds this project hopes to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects. Recent studies conducted by CA Dept. of Fish and Game (CDFG) Natural Stocks Assessment Project (NSA) in the tidal portions of Humboldt Bay tributaries have shown that juvenile salmonids heavily utilize stream-estuary ecotone habitat and routinely rear there for months (CDFG 2010; CDFG 2009; Wallace and Allen 2009; Wallace and Allen 2007). CDFG’s Anadromous Fisheries Research and Monitoring Program (AFRAMP) and NSA projects estimated that about 40% of coho salmon smolts and 80 to 90% of large steelhead smolts originated from the stream-estuary ecotone of Freshwater Creek in 2007 and 2008 (Ricker and Anderson 2011). These studies also showed that juvenile salmonids using this habitat grew faster, obtained a larger size, and likely experienced increased marine survival over juvenile salmonids rearing in stream habitat (Ricker and Anderson 2011; Wallace and Allen 2009; Wallace and Allen 2007; CDFG 2007; Wallace 2006; CDFG 2006; CDFG unpublished data).

Sport Fish Restoration Annual Project Performance Report 2010

Mon, 16 Jul 2018 12:19:32 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the duration of this contract period (2009-2010) NSA continued to sample the tidal portion of Freshwater Creek Slough and Salmon Creek estuary to document their use by juvenile salmonids. NSA also sampled smaller Humboldt Bay tributaries such as Jacoby Creek, Gannon Slough, Martin Slough, Rocky Gulch, and Wood Creek to determine if juvenile salmonids use these very small estuaries as rearing habitat or if they offer over wintering habitat during high stream flow events. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout this project will continue to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects. Prior to CDFG’s Natural Stocks Assessment Project (NSA) study virtually no salmonid sampling had been conducted in the stream-estuary ecotone of Humboldt Bay. On going studies by NSA in the tidal portions of Humboldt Bay tributaries showed that juvenile salmonids heavily utilize stream-estuary ecotone habitat and routinely rear there for months (Wallace and Allen 2009; Wallace and Allen 2007). These studies also showed that juvenile salmonids using this habitat experienced faster growth, obtained a larger size, and likely experienced increased marine survival over juvenile salmonids rearing in stream habitat (Wallace and Allen 2009; Wallace and Allen 2007; CDFG 2007; Wallace 2006; CDFG 2006 and 2005; CDFG unpublished data). Based on data collected by CDFG’s AFRAMP and NSA projects it appears that the stream-estuary ecotone habitat around Humboldt Bay provides extremely important over-winter rearing habitat for juvenile coho salmon and steelhead trout.

Sport Fish Restoration Annual Project Performance Report 2009

Mon, 16 Jul 2018 12:19:18 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the duration of this contract period (2008-2009) NSA continued to sample the tidal portion of Freshwater Creek Slough, Elk River Slough, and Salmon Creek estuary to document their use by juvenile salmonids. NSA also sampled smaller Humboldt Bay tributaries such as Jacoby Creek/Gannon Slough, Martin Slough, Rocky Gulch, and Wood Creek to determine if juvenile salmonids use these very small estuaries as rearing habitat or if they offer over wintering habitat during high stream flow events. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout this project hopes to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects.

Sport Fish Restoration Annual Project Performance Report 2005

Mon, 16 Jul 2018 12:19:04 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - The California Department of Fish & Game’s (CDFG) Natural Stocks Assessment Project (NSA) conducted sampling for juvenile salmonids in Freshwater Creek Slough from July-August 2004 and January to June 2005. NSA also sampled Elk River Slough, Hookton Slough, and Salmon Creek estuary January to June 2005. In Freshwater Creek Slough in 2004 young-of-the-year (yoy) coho salmon were by far the most common salmonid captured and were found primarily in the upper slough. Based on marked and recaptured individuals yoy coho salmon resided in the tidal freshwater portion of Freshwater Slough throughout the summer. All project marked yoy coho salmon were recaptured at the same site where they were originally marked indicating that they moved very little while residing in the slough. Very few juvenile Chinook salmon, steelhead, and cutthroat trout were captured in the upper slough and very few juvenile salmonids were captured in the lower slough during July-August 2004. Beginning in January 2005 NSA resumed sampling in Freshwater Creek Slough and initiated sampling in Elk River Slough and Salmon Creek estuary, Humboldt Bay. In lower Freshwater Creek Slough NSA captured yearling coho salmon from early March to late June and their peak catch occurred in early May. NSA captured yoy coho salmon from early April to mid June and peak catches occurred in late May. NSA captured yoy Chinook salmon from late May to late June and their peak catches occurred in mid June. NSA captured juvenile steelhead from mid March to mid June, with the peak in mid June. In upper Freshwater Creek Slough NSA captured yearling coho salmon from late January to late June and their peak catches occurred late April to early May. NSA captured yoy coho salmon from late April to late June and peak catches occurred in early May. We observed similar catch patterns in lower and upper Elk River Slough. We captured relatively few juvenile salmonids in Hookton Slough and Salmon Creek estuary. Upper Freshwater Creek and Elk River sloughs remain tidal freshwater habitat throughout the year, with water temperatures <18 C. However, the lower sloughs are often brackish during the winter and close to full strength saltwater with water temperature >20 C in the summer and early fall.

Sport Fish Restoration Annual Project Performance Report 2006

Mon, 16 Jul 2018 12:18:52 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During July-December 2005 young-of-the-year (yoy) coho salmon were by far the most common salmonid captured in upper Freshwater Creek and Elk River Sloughs. Based on marked and recaptured individuals yoy coho salmon resided in the tidal freshwater portion of Freshwater and Elk River Sloughs throughout the summer. Most project marked yoy coho salmon were recaptured at the same site where they were originally marked indicating that they moved very little while residing in the sloughs. We captured relatively few juvenile salmonids in lower Freshwater Creek and Elk River Sloughs compared to the upper sloughs during July-December 2005, though we did have modest catches of yoy Chinook during the summer in lower Elk River Slough. During January to June 2006 we captured very few salmonids in Freshwater Creek and Elk River Sloughs prior to May. Yearling coho CPUE peaked in May and yoy coho CPUE peaked in June in both Freshwater Creek and Elk River Sloughs. We captured relatively few salmonids in Hookton Slough and Salmon Creek estuary. Upper Freshwater Creek and Elk River sloughs remain tidal freshwater habitat throughout the year, with water temperatures <18 C. However, the lower sloughs are often brackish during the winter and close to full strength saltwater with water temperature >20 C in the summer and early fall.

Sport Fish Restoration Annual Project Performance Report 2007

Mon, 16 Jul 2018 12:18:40 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the duration of this contract period (2006-2007) NSA continued to sample the tidal portion of Freshwater Creek Slough, Elk River Slough, and Salmon Creek estuary to document their use by juvenile salmonids. Starting in 2007 NSA began sampling smaller Humboldt Bay tributaries such as Rocky Gulch, and Wood Creek to determine if juvenile salmonids use these very small estuaries as rearing habitat or if they offer over wintering habitat during high stream flow events. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout this project hopes to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects.

Sport Fish Restoration Annual Project Performance Report 2008

Mon, 16 Jul 2018 12:18:29 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the duration of this contract period (2007-2008) NSA continued to sample the tidal portion of Freshwater Creek Slough, Elk River Slough, and Salmon Creek estuary to document their use by juvenile salmonids. Starting in early 2007 NSA began sampling smaller Humboldt Bay tributaries such as Jacoby Creek/Gannon Slough, Martin Slough, Rocky Gulch, and Wood Creek to determine if juvenile salmonids use these very small estuaries as rearing habitat or if they offer over wintering habitat during high stream flow events. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout this project hopes to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects.

Jacoby Creek Estuary Field Note March-December 2016

Mon, 16 Jul 2018 12:18:20 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - CA Department of Fish and Game’s (DFG) Natural Stocks Assessment Project (NSA) and City of Arcata staff conducted fish and water quality (WQ) sampling in Jacoby Estuary from March 2016 – December 2016. The sampling was conducted to determine if resident/anadromous juvenile salmonids and other fish species utilize the estuary and lower watershed for rearing and if water quality is adequate to support juvenile salmonids. A comparison site on Jacoby Creek about 150 feet downstream from the estuary mouth (just upstream of the highway 101 bridge) was added to verify the presence of juvenile salmonids in the adjacent creek. An additional comparison site on Jacoby Creek about one-half mile upstream from the estuary mouth was added starting on April 29th 2016 to further verify the presence of juvenile salmonids in the adjacent creek. This information will help us to assess the success of estuarine habitat restoration measures in Jacoby Creek.

Janes Creek-McDaniel Slough Field Note January 2015- May 2016

Mon, 16 Jul 2018 12:18:07 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - City of Arcata and CDFW conducted monthly fish and WQ sampling was conducted to determine if resident/anadromous juvenile salmonids and other fish species utilize the estuary and lower watershed for rearing and if water quality is adequate to support juvenile salmonids. We collected information to establish baseline data about juvenile salmonids and other fish species after the opening of the levee at the mouth of McDaniel Slough. This information will help us to assess the success of estuarine habitat restoration measures in McDaniel Slough.

Janes Creek-McDaniel Slough Field Note October 2013-March 2014

Mon, 16 Jul 2018 12:17:57 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - The City of Arcata and CDFW conducted monthly fish and WQ sampling was conducted to determine if resident/anadromous juvenile salmonids and other fish species utilize the estuary and lower watershed for rearing and if water quality is adequate to support juvenile salmonids. We collected information to establish baseline data about juvenile salmonids and other fish species before and after the opening of the levee at the mouth of McDaniel Slough. This information will help us to assess the success of estuarine habitat restoration measures in McDaniel Slough.

Janes Creek-McDaniel Slough Field Note November 2010-October 2011

Mon, 16 Jul 2018 12:17:46 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - CA Department of Fish and Game’s (DFG) Natural Stocks Assessment Project (NSA) and City of Arcata staff conducted the first in a series of fish and water quality (WQ) sampling in McDaniel Slough and Janes Creek. This field note describes the sampling and presents results from November 2010 to October 2011. Sampling was conducted to determine if resident/anadromous juvenile salmonids and other fish species utilize the estuary and lower watershed for rearing and if water quality is adequate to support juvenile salmonids. We are collecting information to establish baseline data about juvenile salmonids and other fish species prior to the opening of the new tide gates. This information will help us to assess the success of estuarine habitat restoration measures in McDaniel Slough.

Gannon Slough/Jacoby Creek Field Note

Mon, 16 Jul 2018 12:17:35 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - CA Department of Fish and Game’s (DFG) Natural Stocks Assessment Project (NSA) conducted fish and water quality (WQ) sampling in the Gannon Slough and Jacoby Creek estuary complex. Monthly fish and WQ sampling was conducted to determine if juvenile salmonids and other fish species utilize the complex for rearing and if water quality is adequate to support juvenile salmonids. We collected information to establish baseline data about juvenile salmonids and other fish species presence and use of the complex prior to planned restoration work in an effort to measure the success of habitat restoration projects.

Juvenile salmonid use of the tidal portions of selected tributaries to Humboldt Bay, California, 2015-2017

Mon, 16 Jul 2018 12:17:23 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - Pacific States Marine Fisheries Commission and California Department of Fish and Wildlife staff sampled the stream-estuary ecotone (SEE) of selected Humboldt Bay tributaries to document their use by juvenile salmonids and to assess SEE habitat restoration projects. We sampled fish using seine nets and minnow traps baited with frozen salmon roe. Juvenile Coho Salmon (Oncorhynchus kisutch) was the most numerous salmonid captured but we also commonly captured Chinook Salmon (O. tshawytscha), steelhead trout (O. mykiss), and cutthroat trout (O. clarkii clarkii). Subyearling Coho Salmon were present from late March to December with peak catches occurring in the summer and fall. Their mean SEE residence time was one to two months but individual fish reared there for close to a year. Yearling-plus Coho Salmon were present primarily during the winter and spring. One group of Age 1+ Coho Salmon arrived in the SEE in the fall and reared there throughout the winter and into the spring. A later group of Age 1+ Coho Salmon emigrated through the SEE relatively quickly primarily during April and May. Juvenile Chinook Salmon were present primarily in Freshwater Creek Slough in the late spring and early summer. We captured juvenile steelhead trout and cutthroat trout throughout the year and some reared for months, and in the case of cutthroat trout, possibly years in the SEE. Mean growth rates of juvenile salmonids in the ecotone were typically 0.15 to 0.25 mm/day, which was higher than growth rates observed by other projects in stream habitats upstream of the SEE. However, juvenile salmonid growth rates in off channel ponds and in newly constructed slough channels in Wood Creek were usually higher. Juvenile salmonids sought out freshwater rather than brackish water habitat while rearing in the SEE. Juvenile salmonids, especially Coho Salmon, utilized newly constructed off channel habitat as soon as they were completed and fall/winter stream flow converted the areas to fresh water habitat. Finally, PSMFC staff developed a series of computer programs to more easily process, summarize, and analyze large data sets of PIT tag antenna data. This subject is covered in Section 2 of this report.

Juvenile salmonid use of Freshwater Slough and tidal portion of Freshwater Creek, Humboldt Bay, California 2003 annual report

Thu, 21 Jun 2018 08:24:49 -0700

tidal and freshwater ecotone juvenile salmonid monitoring - The California Department of Fish and Game’s (CDFG) Natural Stocks Assessment Project (NSA) sampled juvenile salmonids in Freshwater Creek Slough, Humboldt Bay from March through October 2003 to determine their migration timing and use of estuarine habitat. This report covers the first year of a planned multi-year field study. NSA staff used seine nets to capture fish in the main channel of the slough and fyke traps to sample tidal meanders and a restored marsh adjacent to the slough. In the upper slough, NSA personnel captured yearling coho salmon, Oncorhynchus kisutch, in mid March and from mid May until late June. Their peak catch occurred in mid March with a smaller peak in late May. NSA staff captured young-of-the-year (yoy) coho salmon from mid May until late October; peak catches occurred in early July. Field crews captured yoy Chinook salmon, O. tshawytscha, from mid May until early August; peak catches occurred in early June. In the lower slough, yearling coho were captured from early April until early July, with peak catches occurring mid to late May. NSA crews captured yoy coho salmon mostly in early April and then in low numbers until mid June. NSA staff captured yoy Chinook salmon from early April until mid July, with peak catches occurring in mid June. Yearling coho were longer in size in the lower slough than in the upper slough. The mean fork length(FL) of yoy coho salmon residing in the upper slough was longer than those in Freshwater Creek upstream of the estuary. The average length of estuarine residence for mark/recaptured fish was 1 week (range 1-3 weeks) for yearling coho salmon and 4 weeks (range 1-8 weeks) for yoy Chinook salmon. Yoy Chinook salmon recaptured in the lower slough had a longer average estuarine rearing time than those recaptured in the upper slough. Mark/recaptured yoy coho salmon reared in the upper slough for up to 11 weeks after marking.

Initial study and negative declaration for the lake siskiyou net pen project at Lake Siskiyou, Siskiyou County

Mon, 30 Apr 2018 14:57:13 -0700

Initial Study-CEQA - The purpose of the Lake Siskiyou Net Pen Project (LSNPP) is to enhance Lake Siskiyou’s fishery to benefit anglers by creating excitement about the creation of a trophy trout program. The goal of the project is to increase angler participation, namely with youth and families, through incentivized fishing by providing better opportunity to catch trophy sized trout. Furthermore, this project will provide community education opportunities about fisheries and wildlife management through interpretive signage near the net pens and hosted community events. The project will use a portion of the already existing trout stocking allotment, place trout in net pens for approximately 30 weeks, and feed them an optimum diet based on their size and water temperatures, until their eventual release into the reservoir.

Mill Creek salmonid lifecycle monitoring station juvenile Coho Salmon outmigrant trapping project 2014-2017, Smith River, California

Wed, 03 Jan 2018 08:56:12 -0800

Coastal Salmonid Monitoring Program, Smith River - We used spring outmigrant trapping data to estimate the abundance of salmonid smolts emigrating from Mill Creek, Smith River (California), over four years from 2014 to 2017. We also estimated the apparent overwinter survival probability of Coho Salmon(Oncorhynchus kisutch) marked during the fall of 2013-2016 in Mill Creek and its two primary subbasins, East Fork Mill Creek and West Branch Mill Creek, using data collected by California Department of Fish and Wildlife. We operated a rotary screw trap (RST) in lower Mill Creek from mid-March through late June each year. Young-of-the-year Chinook Salmon (Oncorhynchus tshawytscha)were the most numerous fish captured during all four seasons (5319, 47399, 114797 and 56969 individuals during 2014-2017) followed by unidentified trout (3148, 3377, 3341 and 2341 individuals during 2014-2017). We captured a total of 2188, 3529, 2207 and 1542 Coho Salmon smolts and 266, 383, 1158 and 699 young-of-the-year Coho Salmon in the rotary trap during 2014-2017. We captured a total of 1464, 2579, 1752 and 1857 steelhead (Oncorhynchus mykiss) and 751, 1464, 760 and 1102 Coastal Cutthroat Trout (Oncorhynchus clarki clarki) during 2014-2017. Markrecapture of fin clipped smolts was used to estimate the abundance of Coho Salmon, steelhead, and Coastal Cutthroat Trout emigrants passing the trap site. We estimated a total of 7416 (95% CI: 6580-8251), 8195 (95% CI: 7342-9047), 7567 (95% CI: 6706-8427) and 9383 (95% CI: 6349-12418) spring migrant Coho Salmon smolts emigrated past the Mill Creek outmigrant trapping site in 2014, 2015, 2016 and 2017 respectively. We estimated a total of 1075 (95% CI: 695-1456), 2554 (95% CI: 1931-3176), 2078 (95% CI: 1159-2997) and 3882 (95% CI: 1944-5820) steelhead smolts emigrated in 2014, 2015, 2016, and 2017, respectively. We estimated a total of 340 (95% CI: 191-488), 4175 (95% CI:3144-5205), 2427 (95% CI: 1315-3539) and 5423 (95% CI: 3536-7310) Coastal Cutthroat Trout smolts emigrated in 2014, 2015, 2016, and 2017 respectively. We used Cormack-Jolly-Seber (CJS) mark recapture models to estimate the ‘apparent’ overwinter survival and early emigration (individuals emigrating prior to the installation of the RST) of Coho Salmon tagged in the previous fall by using the recaptures at the RST and three stationary PIT tag antenna arrays in Mill Creek and two arrays located in the Smith River estuary. Apparent overwinter survival, ranged from 6.0%-12.8% throughout the Mill Creek basin, 4.2%-12.9% for West Branch Mill Creek, 7.2%-14% for East Fork Mill Creek and 3.5%-6.3% for mainstem Mill Creek. Minimum annual early emigrants comprised on average 20.6% (15.2%-26.2%) of fall tagged fish recaptures in Mill Creek, showing significant numbers of Coho Salmon juveniles emigrated early. Estuary antenna detections during 2015 thorough 2017 showed 46.2% (34.9%-57.5%) of early Mill Creek emigrants used these habitats.

Results of Freshwater Creek Salmonid Life Cycle Monitoring Station 2015-2016

Mon, 09 Oct 2017 14:54:37 -0700

salmonid lifecycle monitoring station - The California Department of Fish and Wildlife (CDFW) and the National Oceanic and Atmospheric Administration ~ Fisheries (NOAA~Fisheries) cooperatively developed the draft Coastal California Salmonid Monitoring Plan (CMP). Two complimentary tasks are considered high priority in the Northern Monitoring Area and form the foundation of the CMP approach. The first task consists of probabilistic sampling of stream reaches within a defined region using spawning ground surveys (SGS) to establish the regional status and trends of adult salmonid abundance. The second task develops intensively monitored Life Cycle monitoring Stations (LCS) nested within the regional sample frame of the SGS. LCS studies have 4 primary objectives: Define the relationship between SGS observations and adult escapement, Estimate juvenile and adult abundance, and freshwater and marine survival rates. Provide a study framework to investigate habitat-productivity relationships Characterize the diversity of life history patterns. The Freshwater Creek Salmonid Monitoring Project is designed to be a LCS with these principal objectives. This report summarizes the results of yearly abundance and survival monitoring efforts from October 2015 to June 2016, as well as integrates project data to make inference on population trends and limiting factors for coho salmon in Freshwater Creek.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in the Humboldt Bay, Humboldt County California, 2015-2016

Mon, 09 Oct 2017 14:42:58 -0700

spawning survey - Field staff conducted spawning ground surveys in 23 reaches within the Humboldt Bay watershed between November 17, 2015 and April 21, 2016. Individual stream reaches were surveyed an average of 4.1 times at an average return interval of 29 days. We observed 2 Chinook salmon, 740 coho salmon, 34 steelhead trout, and 23 unidentified live fish. A total of 2 Chinook salmon, 339 coho salmon, 2 steelhead trout, and 53 unidentified carcasses were found. We identified 454 individual redds of which 171 were assigned to a species. We estimate 617 (430-849, 95% Confidence Interval) coho redds and 97 (21-184, 95% Confidence Interval) steelhead redds in Humboldt Bay as expanded from the sampled reaches. We estimate 323 (251-394, 95% Confidence Interval) coho redds within the Freshwater Creek Life Cycling Monitoring Station as the sum of a complete census of all reach estimates.

Results of regional spawning ground surveys and estimates of total salmonid redd construction in Redwood Creek, Humboldt County California, 2015-2016

Mon, 09 Oct 2017 14:41:44 -0700

spawning survey - Field staff conducted spawning ground surveys in 24 reaches within the Redwood Creek watershed between November 16, 2015 and March 28, 2016. Individual stream reaches were surveyed an average of 5.1 times at an average return interval of 23 days. We observed 389 Chinook salmon, 89 coho salmon, 59 steelhead trout, and 40 unidentified live fish. A total of 125 Chinook salmon, 32 coho salmon, 0 steelhead trout, and 41 unidentified carcasses were found. We identified 704 individual redds of which 173 were assigned to a species. Redwood Creek redd abundance estimates of Chinook salmon, coho salmon, and steelhead trout with 95% confidence intervals are 740 (427, 1200), 206 (146,313), and 283 (132,488) respectively.

Juvenile Coho Salmon detections in an Unnamed Tributary to the Smith River, Smith River, California.

Thu, 16 Mar 2017 14:42:20 -0700

coho salmon and barriers in the Smith River coastal plain - A total of 17 locations were sampled for juvenile salmonids and water quality throughout the lower 920 meters of stream from Fred Haight Drive to the Smith River. Additional sites within the stream (located near Highway 101) were sampled on an earlier later date and yielded no salmonids. The entire stream contained water during the time of the survey to the mouth where the stream went subsurface at an exposed gravel bar along the Smith River. A total of 110 juvenile coho salmon were found throughout the survey reach in 13 of the 17 sample locations. An average of 8.5 coho salmon were captured per trap and ranged from one to 33 individuals per trap. The average length of captured coho was 85mm (range: 61 to 108 mm). The trap location containing the most coho salmon was in a ponded portion of the stream above a culvert partially dammed by a beaver. A total of eight juvenile trout (cutthroat or steelhead) were captured at five locations and one threespine stickleback was observed. A total of five road crossings with culverts were located throughout the survey reach (Figure 2). All crossings were identified as temporal juvenile salmonid barriers due to culverts being undersized,perched, improperly aligned with the stream channel, plugging with debris, and/or failing (culvert invert rusting out).

Hatchery and genetic management plan for Mad River Hatchery winter-run steelhead

Thu, 09 Mar 2017 14:24:26 -0800

Fish Hatchery Management - The Mad River Hatchery’s Hatchery and Genetic Management Plan, HGMP, was approved February 2017. This document adheres to the guidelines recommended by National Marine Fisheries Service (NMFS, aka NOAA Fisheries) (2003a) in Updated July 2000 4(d) Rule Implementation Binder for Threatened Salmon and Steelhead on the West Coast for development of an HGMP. This document describes how CDFW will manage the Mad River Hatchery’s, MRH, winter-run steelhead trout program as an integrated program, with conservation potential, because 1) gene flow from Hatchery Origin, HOR, to Natural Origin, NOR, stocks cannot be eliminated, though with increased monitoring it may be possible to further understand HOR to NOR gene flow, and 2) continued use of NOR fish as broodstock (i.e., integrated program management) will reverse genetic drift in the hatchery stock. Increasing the integration of NOR fish into MRH will also help increase the PNI (Proportionate Natural Influence), and help insure that natural selective forces (e.g. PNI > 0.50), rather than hatchery selective forces, dominate. This integrated approach can provide opportunity for hatchery-based recovery of genetically compatible fish. Additional information will describe the interrelationship and interdependence of the program with fisheries management.

Winter Distributions, Movements, and Habitat use by Juvenile Salmonids throughout the Lower Smith River Basin and Estuary, Del Norte County, California

Thu, 09 Mar 2017 14:15:40 -0800

Coastal Salmonid Monitoring Program, Smith River - Properly functioning estuaries are complex systems where aquatic organisms benefit from a variety of spatial and temporal niches. This is especially evident for Pacific juvenile salmonids, where studies have shown estuarine habitats can be more productive and can lead to greater growth and survival compared to those derived from natal stream habitats occurring upstream. Habitats including low gradient streams, sloughs, backwaters, off channel ponds, and emergent tidal wetlands have been shown to be especially productive features for rearing juvenile salmon throughout California and the Pacific Northwest. Understanding the functional role of coastal streams and estuaries can aid management and restoration decisions in maximizing population resilience through protection of diverse life-history patterns expressed among various salmonid populations. To fully understand current and potential life-history variation in individual salmonid populations, intensive studies designed to describe the spatial and temporal distribution of salmonids, their respective habitats, and potential limiting factors are needed. This information can then be used towards the goal of recovering populations by maximizing life-history variation through various habitat restoration and conservation strategies. The first year of this study (Parish and Garwood 2015) included both summer and winter periods and found salmonid distributions, especially coho salmon, were more widespread throughout the estuary and coastal plain during the winter when temporary streams and slough channels maintained water. Additional summer salmonid distribution monitoring has occurred since 2012 throughout the Smith River basin (Garwood and Larson 2014, Garwood et al. 2014, Walkley and Garwood 2015). This second winter sampling effort was initiated to fill in salmonid distribution gaps since only 45% of the total winter estuary sampling frame was surveyed in 2015 (Parish and Garwood 2015). We were also motivated to revisit productive salmonid rearing sites identified during the winter of 2015 to assess their use over a range of environmental conditions and across separate cohorts.

2011-2016 Salmonid Redd Abundance and Juvenile Salmonid Spatial Structure in the Smith River Basin, California and Oregon

Thu, 09 Mar 2017 14:02:07 -0800

Coastal Salmonid Monitoring Program, Smith River - We investigated two essential population viability metrics of salmonids over five consecutive years in the Smith River basin (Oregon and California), with ESA listed coho salmon as the focal species. First, we monitored adult salmonid escapement and distribution from 2011 to 2016 using live fish, carcass, and redd counts as defined in California’s Coastal Salmonid Monitoring Plan. Second, we estimated the summer spatial structure of juvenile salmonids and adult coastal cutthroat trout annually from 2012 to 2016 using multiple-pass snorkel surveys in an occupancy modeling framework. We constructed separate sample frames for each monitoring component using a reproducible approach that relied on empirical and modeled stream habitat information. Each sample frame was divided into survey reaches resulting in 161.8 kilometers of stream habitat (68 reaches, 30 sub-reaches) for the adult sample frame and 298.1 kilometers (126 reaches, 40 sub-reaches) for the juvenile spatial structure sample frame. We estimate the adult sampling frame covered 78% of potential coho salmon spawning habitat and the juvenile sampling frame covered essentially all likely summer juvenile coho salmon rearing habitats. This report provides detailed results from the 2015-2016 survey effort not reported previously as well as five-year summaries spanning the length of this monitoring effort. This document is also supported by previously published reports offering greater detail on annual results (i.e. Garwood and Larson [2014], Garwood et al. [2014] and Walkley and Garwood [2015]). We completed 1896 spawning ground surveys across 87 survey reaches over the five years representing a sum total of 3346 kilometers surveyed. Detailed results are reported for all salmonids. Hatchery origin Chinook salmon and steelhead were observed spawning throughout much of the sampling frame over the five years, especially in Rowdy Creek and Mill Creek. The mean hatchery proportion of Chinook salmon carcasses ranged from 8.8% in tributaries below the Smith River forks to 32.9% in Rowdy Creek. The mean hatchery proportion of live steelhead ranged from 5.3% below the forks to 28.6% in Rowdy Creek. We used multi-scaled occupancy models to estimate the probability of salmonid occupancy at the sample reach and at the sample unit (within reach) simultaneously while accounting for species detection probabilities. From 2012 to 2016 we completed a 323 reach surveys totaling 608 cumulative stream kilometers within the Smith River. We sampled 7254 pools over the five years with annual totals ranging from 1115 pools to 1837 pools. Detailed results are reported for all species. We describe five extant juvenile coho salmon patches. Four of the five patches are maintained by independent spawning sub-populations and we consider the lower mainstem Smith River and tributaries to be the only significant non-natal coho salmon rearing patch.

2014-2015 Salmonid Redd Abundance and Juvenile Salmonid Spatial Structure in the Smith River Basin, California and Oregon

Thu, 09 Mar 2017 13:32:19 -0800

Coastal Salmonid Monitoring Program, Smith River - We continued to investigate two population viability metrics of salmonids in the Smith River basin (California and Oregon), with ESA listed coho salmon as the focal species. First, we monitored adult salmonid escapement and distribution for a fourth year during the winter of 2014-2015 using a combination of live fish, carcass, and redd counts as defined in California’s Coastal Salmonid Monitoring Plan. We completed 414 spawning ground surveys in 30 main reaches and 11 sub-reaches throughout the Smith River basin during the 2014-2015 season. We made 216 live adult coho salmon observations. Most coho salmon observations occurred in Mill Creek with the exception of six individuals observed in Rowdy Creek. We recovered 15 coho salmon carcasses, all of which were observed in Mill Creek. Last, we were able to verify 39 individual coho salmon redds. As with previous years, all verified redds were found clustered in the upper Mill Creek sub-basin so we restricted the coho salmon redd population estimate to Mill Creek to avoid excessive error associated with between-reach sampling variation. We estimated total coho salmon redd abundance in the Mill Creek sub-basin as 149 (95% CI: 139 - 159) redds which equaled 31%, 66% and 57% of the estimated number of redds produced in the three previous seasons. Chinook salmon and steelhead total redd abundance estimates were determined for the sample frame since these species were more evenly distributed throughout the Smith River basin. We estimated Chinook salmon redd abundance as 1715 (95% CI: 1092 - 2337) which equaled 45%, 96%, and 332% of the estimated number of redds produced in the three previous seasons. Steelhead redd abundance estimates are incomplete since we only surveyed approximately 60% of the season. However, we estimated a total of 914 steelhead redds (95% CI: 381 - 1446) equaling 87%, 132% and 257% of the estimated number of redds produced in the three previous incomplete survey seasons. Hatchery origin salmonids were observed spawning throughout sampling frame below the major river forks, with the mean hatchery proportion of Chinook salmon carcasses ranging from 0% to 42% and mean hatchery proportion of live steelhead ranging from 0% to 25%. Second, we monitored the summer spatial structure of juvenile salmonids and adult coastal cutthroat trout for a fourth year during the summer of 2015 using multiple-pass snorkel surveys in an occupancy modeling framework. We detected juvenile coho salmon 21 out of 69 surveyed reaches in four portions of the watershed. Ten (48%) of the reaches with coho salmon were determined non-natal rearing areas. Estimated large-scale occupancy of juvenile coho salmon equaled 0.31 (SE=0.06) while estimated small-scale occupancy equaled 0.68 (SE=0.03) resulting in a proportion of total area occupied (PAO) of 0.21. Juvenile Chinook salmon had an estimated PAO of 0.35, over twice that of PAO estimates for 2014, but similar to those from 2012 and 2013.

2013-2014 Salmonid Redd Abundance and Juvenile Salmonid Spatial Structure in the Smith River Basin, California and Oregon

Thu, 09 Mar 2017 13:17:20 -0800

Coastal Salmonid Monitoring Program, Smith River - We continued to investigate two population viability metrics of salmonids in the Smith River basin (California and Oregon), with ESA listed coho salmon (Oncorhynchus kisutch) as the focal species. First, we monitored adult salmonid escapement and distribution for a third year during the winter of 2013-2014 using a combination of live fish, carcass, and redd counts as defined in California’s Coastal Salmonid Monitoring Plan. We completed 343 spawning ground surveys in 36 main reaches and 13 sub-reaches throughout the Smith River basin during the 2013-2014 season. We made 494 live adult coho salmon observations. We recovered 54 coho salmon carcasses. All coho salmon carcasses were observed in Mill Creek except four individuals in Rowdy Creek. We were able to verify 108 individual coho salmon redds. We estimated total coho salmon redd abundance in the Mill Creek sub-basin as 260 (95% CI: 253 - 266) redds which equaled 54% and 115% of the estimated number of redds produced in the two previous seasons. Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) total redd abundance estimates were determined for the sample frame since these species were more evenly distributed throughout the Smith River basin. We estimated Chinook salmon redd abundance as 516 (95% CI: 284 - 770) which equaled only 14% and 29% of the estimated number of redds produced in the two previous seasons. Steelhead redd abundance estimates are incomplete since we only surveyed approximately 60% of the season. However, we estimated a total of 356 steelhead redds (95% CI: 212 - 502) equaling 34% and 51% of the estimated number of redds produced in the two previous incomplete survey seasons. Hatchery origin salmonids were observed spawning throughout sampling frame below the major river forks, with the mean hatchery proportion of Chinook salmon carcasses ranging from 0% to 42% and mean hatchery proportion of live steelhead ranging from 0% to 25%. Second, we monitored the summer spatial structure of juvenile salmonids and adult coastal cutthroat trout (Oncorhynchus clarki clarki) for a third year during the summer of 2014 using multiple-pass snorkel surveys in an occupancy modeling framework. We detected juvenile coho salmon in 23 out of 67 surveyed reaches in five portions of the watershed. Eight (35%) of the reaches with coho salmon were determined non-natal rearing areas. Estimated large-scale occupancy of juvenile coho salmon equaled 0.35 (SE=0.06) while estimated small-scale occupancy equaled 0.67 (SE=0.02) resulting in a proportion of total area occupied (PAO) of 0.23. Juvenile Chinook salmon had an estimated PAO of 0.15, equaling only 56% and 42% of previous years. This large reduction of Chinook salmon space use could be related to early smolt migration timing, but was likely more influenced by the small adult return in the previous winter coupled with an extended drought period observed during the previous winter limiting spawning distributions.

2015-2016 Chinook salmon dewatered redd monitoring on the Sacramento River

Wed, 27 Jul 2016 09:39:13 -0700

Salmon reproduction and drought - California’s extensive water delivery system requires elevated Sacramento River flows during summer months and a reduction of flows starting in late summer to conserve storage for the following year. California’s unprecedented drought has severely limited stored water in Shasta Reservoir, further emphasizing the importance of conserving stored water. As a result, Chinook salmon spawning downstream of Keswick Dam are subject to redd dewatering as flows are reduced. Overlapping winter-run incubation times and fall-run spawning periods allowed fall-run redds to be built before flows were reduced, increasing dewatering potential. Our monitoring effort marked and revisited redds which were deemed vulnerable to dewatering, re-measuring depth as flows out of Keswick Dam were reduced. Additionally, marked redds were categorized by the degree and duration of dewatering, indicating effect on juveniles. We observed 291 dewatered fall-run redds and one spring -run redd during the 2015-2016 survey period, a dewatering rate of 2.14%. Assuming a fecundity of 5,407 eggs per female (USFWS, 2012), 100% potential egg to fry survival, and 100% mortality, dewatering is theoretically responsible for a reduction in recruitment of 1,573,437 juvenile fall-run Chinook and 5,407 juvenile spring -run Chinook. It is unclear whether 100% mortality can be assumed, therefore additional research should be conducted to further clarify exactly what impact different degrees of dewatering have on Chinook redds in the Sacramento River.

Distribution of Juvenile Salmonids and Seasonally Available Aquatic Habitats within the Lower Smith River Basin and Estuary, Del Norte County, California

Thu, 17 Dec 2015 14:31:03 -0800

Coastal Salmonid Monitoring Program, Smith River - This study was designed to assess current spatial structure of salmonids occurring in unique non-natal rearing habitats that have yet to be studied in detail within in the lower Smith River and estuary. Results from this baseline assessment provide detailed information regarding the distribution, seasonal occurrence, and habitat associations of juvenile coho salmon and other salmonid species. Identifying limiting factors and uncertainties associated with juvenile coho salmon rearing habitat in the lower Smith River basin will aid in prioritizing habitat restoration and recovery of the species.

A Regional Approach for Monitoring Salmonid Status and Trends: Results from a Pilot Study in Coastal Mendocino County, California

Wed, 24 Apr 2013 10:55:28 -0700

regional salmonid monitoring CMP - Abstract.—In coastal California, many evolutionarily significant units (ESUs) of Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss are listed under the federal Endangered Species Act (ESA). Monitoring species status at the ESU or ESU subdivision scale requires specialized sampling. The purposes of this study were (1) to evaluate abundance estimated from a generalized random tessellation stratified (GRTS) design and compare the results with those from a more intensive stratified random monitoring program and (2) to evaluate the statistical power of the design to detect population trends. This 3-year pilot study considered five Mendocino County streams as an example region of coastal California to evaluate a two-stage sampling approach for monitoring regional escapement. Under this scheme, regional redd surveys (stage 1) were conducted in stream reaches in a GRTS sampling design. Ten percent of anadromous habitat was sampled in year 1 and 10–35% in years 2 and 3. Spawner : redd ratios were derived from smaller-scale census watersheds (stage 2) where ‘‘true’’ escapement was estimated using capture–recapture methods. Regional escapement was then estimated from expanded redd counts, calibrated by spawner : redd ratios. As an alternative, more intensive method for estimating escapement, three survey streams were also sampled in a stratified random design. The results, added to counts from the census basins, produced more rigorous ‘‘sum-of-streams’’ estimates for comparison with the GRTS sampling. Redd counts and the resulting escapement estimates were reliable for regional monitoring. The GRTS and sum-of-streams estimates overlapped, and the variation in the 95% confidence intervals did not change after 15%. Our results suggest that a sample size of 15% or 41 or more reaches (whichever results in fewer survey reaches) should have adequate precision and statistical power to detect regional trends in salmon populations. We recommend that this monitoring approach be applied at regional spatial scales consistent with ESA recovery planning efforts.

Performance of Spawner Survey Techniques at Low Abundance Levels

Wed, 24 Apr 2013 10:55:04 -0700

Coastal salmon escapement monitoring - Abstract.—Population monitoring is essential to know whether coastal California’s Endangered Species Act–listed Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss stocks are progressing toward recovery. In coastal California, salmonids are at the southern edge of their range, and this one of many reasons they are not abundant. This provides unique challenges for monitoring, as different survey methods will result in estimates with different levels of accuracy and precision, which are important for evaluating population trends. For this study we intensively monitored three Mendocino County watersheds to evaluate the reliability of two-stage data for monitoring regional escapement. Under this scheme, regional spawning surveys (stage 1) were calibrated with data from intensively monitored watersheds (stage 2), where escapement was estimated using capture–recapture methods, redd counts, and fish counts. The objective of the study was to evaluate the quality of the stage 2 data for calibrating regional surveys. We evaluated the precision of live-fish capture–recapture estimates and compared these estimates with estimates derived from spawning survey data using carcass capture–recapture, area under the curve (AUC), and redd counts. Live-fish capture–recapture produced escapement estimates with narrower 95% confidence bounds where permanent structures were used to capture fish. Redd counts converted to fish numbers using spawner : redd ratios were chosen for the regional salmonid monitoring method because they were reliable, economical, and less intrusive. Converted redd counts were statistically and operationally similar to live-fish capture– recapture estimates but required fewer resources. The AUC estimates were less reliable than converted redd counts and live-fish capture–recapture methods due to the sensitivity of the estimates of residence time and observer efficiency. Finally, we found that carcass capture–recapture methods were operationally unsuccessful in coastal California streams. On the basis of our results, we recommend that annual spawner : redd ratios from intensively monitored watersheds be used to calibrate redd counts for regional status and trend monitoring of California’s coastal salmonids.

Mendocino coast regional salmon monitoring 2009

Tue, 23 Apr 2013 15:10:31 -0700

salmonid monitoring and escapment - This report documents the results of the first year of a multi-year regional salmonid monitoring program the first implemented part of the California’s Coastal Salmonid Monitoring Program (CMP), funded by the Fisheries Restoration Grants Program. The scope of the work was to monitor salmonid (Chinook salmon, Coho salmon, and Steelhead) escapement in all coastal streams in Mendocino County to develop regional and watershed specific population estimates and continue life cycle monitoring in three streams. We used annual spawner: redd ratios from life cycle monitoring streams to calibrate regional redd counts and to ensure sufficient statistical power and adequate precision in the results. We sampled 41 reaches in a Generalized Random Tessellation Stratified (GRTS) design. We estimated 517 (95% CI 212-909) coho salmon redds and 887 (95%CI 415-1545) adult coho salmon and 1143 (95% CI 634-1749) steelhead redds and 442 adult steelhead (95% CI 245-674) in coastal Mendocino County during 2008-09.

Redd Counts

Tue, 23 Apr 2013 15:10:05 -0700

redd counts - The purpose of this protocol is to describe field methods for the consistent collection of salmonid redd abundance and subsequent estimation of adult salmonid breeding population size. We recommend surveys be conducted on predetermined, 3–5-km long stream reaches, using a spatially balanced rotating panel design. We suggest an annual draw of 10% of all reaches in the sampling universe as the target goal for monitoring; furthermore, to account for access problems and other barriers to sampling, we recommend that the initial sample draw should over-select reaches (sampling rate of 25%) to provide flexibility in the field. One field survey should occur prior to fish entering the spawning areas, with surveys thereafter conducted 7–14 d apart until new fish and redds are no longer observed. Surveyors will need to recognize that stream flows and/or weather conditions will have some bearing on the temporal aspects of surveys. All redds will be identified to species, measured, and georeferenced. Redd longevity and observer efficiency in redd detection will be estimated for each watershed by tracking the condition of individual redds measured during previous surveys. To document sex ratios, the sex of all live fish will be visually identified on behaviors at redds or other visual cues (dead fish will be identified, sexed, inspected for tags, and measured, per the carcass count protocol, page 59). In situations where multiple salmonid species overlap on a given spawning area, redd sizes will help differentiate the species involved.

Discrimination of Chinook Salmon, Coho Salmon, and Steelhead Redds and Evaluation of the Use of Redd Data for Estimating Escapement in Several Unregulated Streams in Northern California

Tue, 23 Apr 2013 15:09:20 -0700

redd counts auc escapement - We developed and evaluated a stratified index redd area method to estimate Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss escapement in several coastal streams in northern California based on the assumption that redd size is related to the number of redds a female builds. Sources of error in redd counts were identified, including the use of logistic regression to classify redd species (necessary due to temporal overlap in the spawning of these species in coastal northern California). Redd area escapement estimates were compared with estimates from more conventional methods and releases above a counting structure. Observer efficiency in redd detection ranged from 0.64 (SE 5 0.10) to 0.75 (SE 5 0.14) and was significantly associated with streamflow and water visibility (analysis of variance [ANOVA]: F 5 41.8; P , 0.001). Logistic regression reduced uncertainty in redd identification. Redd area and date observed were significant in predicting coho salmon and steelhead redd species (Wald’s z 5 11.9 and 18.09, respectively; P , 0.001). Pot substrate and redd area were significant in classifying Chinook and coho salmon redds (Wald’s z 5 5.88 and 4.03; P 5 0.015 and 0.04, respectively). Stratified index redd area escapement estimates and estimates based on capture–recapture experiments, area-under-the-curve estimates, and known releases above the counting structure (coho salmon only) were not significantly different (ANOVA: F , 13.6; P . 0.06). Escapement estimates assuming one redd per female were only significantly different from other methods for steelhead (ANOVA: F 5 13.11; P 5 0.006). Redd counts were significantly correlated with escapement estimates (r . 0.82; P , 0.04). Reduction of counting errors and uncertainty in redd identification, biweekly surveys throughout the spawning period, and the use of redd areas in a stratified index sampling design produced precise, reliable, and cost-effective escapement estimates for Chinook salmon, coho salmon, and steelhead.

Measurement of key life history metrics of coho salmon in Pudding Creek, California

Mon, 04 Jun 2012 15:30:16 -0700

coho salmon life history - Since 2005, a life cycle monitoring project in Pudding Creek, California, has utilized a variety of methodologies including an adult trap, spawning surveys, PIT tags, electro-fishing, and a smolt trap to estimate coho salmon adult escapement, juvenile abundance, juvenile growth, winter survival, and marine survival. Adult coho salmon escapement and smolt abundance are closely related when spawner abundance is high. However, with decreasing escapement, smolt abundance appears to stabilize. Adult abundance has declined dramatically, from 1200 in 2005 to 20 in 2010. Corresponding smolt abundance initially declined from 24,000 to approximately 15,000 but maintained at that level despite continued declines in escapement. Winter survival ranged from 17 to 80 percent, and appeared to increase as the juvenile population decreased. Juvenile growth rates within the upper watershed were low during summer and significantly higher in spring and fall. PIT tag detections indicated that thirteen percent of all coho outmigrants were two year old smolts that were smaller at tagging than one year old outmigrants, but larger than one year old fish at outmigration. Over three complete coho life cycles (2006 to 2010), ocean survival appeared to strongly affect adult returns. In all years since 2006, ocean survival for Pudding Creek spawners was notably lower than reported by others in streams throughout the Pacific Northwest in previous years.

How do we know how many salmon returned to spawn? Implementing the California coastal salmonid monitoring plan in Mendocino County, California

Mon, 04 Jun 2012 15:26:29 -0700

Coastal salmon escapement monitoring - California’s coastal salmon and steelhead populations are listed under California and Federal Endangered Species Acts; both require monitoring to provide measures of recovery. Since 2004 the California Department of Fish and Game and NOAA Fisheries have been developing a monitoring plan for California’s coastal salmonids (the California Coastal Salmonid Monitoring Plan- CMP). The CMP will monitor the status and trends of salmonids at evolutionarily significant regional scales and provide population level estimates. For the CMP, data to evaluate adult populations are collected using a spatially balanced probabilistic design (e.g., Generalized Random Tesselation Stratified- GRTS). Under this scheme a two stage approach is used to estimate status. Regional redd surveys (stage 1) are conducted in stream reaches in a GRTS sampling design at a survey level of 15 percent or = 41 reaches, which ever results in fewer reaches, of available habitat each year. Spawner: redd ratios are derived from smaller scale census watersheds (stage 2) where “true” escapement is estimated using capture-recapture methods. These are used to estimate regional escapement from expanded redd counts. In 2008 and 2009 we applied the results of our previous studies to estimate salmonid escapement for the Mendocino coast region, the first implementation of the CMP in the state. Here we present the results of the first 3 years of this monitoring effort and discuss our findings in context of expanding the CMP to all of coastal California. We discuss sample frame development, sample size, and present escapement data for six independent and eight potentially independent populations and two Diversity Strata within the Central California Coho Salmon Evolutionarily Significant Unit.

Ocean Ranch Unit, Eel River Wildlife Area Tidal Marsh Geometry Analysis

Tue, 16 Aug 2011 11:24:10 -0700

Tidal marsh geometry analysis - Tidal datums were computed from water level measurements at four sites within and adjacent to the ORU. Based on findings, recommends using the San Francisco Bay relations (PWA 2004) for estimating tidal prism, channel top width, and cross-section area for marsh areas greater than 4.9 acres, and Mad River Slough relations for marsh areas less than 4.9 acres for channel designs rather than using site specific relations measured within the ORU. Provides a first approximation of areas that are likely to develop a channel network by levee breaching relative to areas that may require mechanical excavation to re-develop a channel network.

Prospectus for and Eel River Management Area

Fri, 24 Jun 2011 07:56:05 -0700

CalFish collection. Contact cshannon@dfg.ca.gov for assistance. - The essential function of the California State Division of Fish and Game is to insure the exploitation of the State's fish and game resources in such a way that the maximum sustained yield will be obtained. In this task the several Bureaus of the Division have their special functions to perform. It is the function of the Bureau of Fish Conservation to provide the maximum in the way of sport fishing in the inland waters. In order to fulfill its function, the Bureau of Fish Conservation must possess certain knowledge. This consists of (1) a basic knowledge of the life histories of the fresh-water and anadromous fishes, (2) a basic knowledge of the streams and lakes of the State, (3) a knowledge of the fisheries in existences and of the wants of the fishermen, and (4) a knowledge of the methods by which the stock of freshwater fishes may be maintained and the desired type of fishing supplied to the anglers. As this knowledge is accumulated, it will be possible to modify the practices now in existence and to put into effect new practices. Once the worth of the recommended practices is decided upon, limiting factors in their execution will be legislation, funds, and man power.

Juvenile salmonid use of the tidal portions of selected tributaries to Humboldt Bay, California, 2007-2009

Tue, 15 Jun 2010 08:35:38 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring - During the duration of this contract period (2007-2009) NSA continued to sample the tidal portion of Freshwater Creek Slough, Elk River Slough, and Salmon Creek estuary to document their use by juvenile salmonids. Starting in early 2007 NSA began sampling smaller Humboldt Bay tributaries such as Jacoby Creek/Gannon Slough, Martin Slough, Rocky Gulch, and Wood Creek to determine if juvenile salmonids use these very small tidal streams as year round habitat or over winter rearing habitat during high stream flow events. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout this project hopes to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects.

Juvenile salmonid use of the tidal portions of selected tributaries to Humboldt Bay, California

Tue, 15 Jun 2010 08:35:19 -0700

Humboldt Bay tributaries tidal and freshwater ecotone juvenile salmonid monitoring 2005-2007 - During the duration of this contract period (2005-2007) the California Department of Fish & Game’s (CDFG) Natural Stocks Assessment Project (NSA) continued to sample the tidal portion of Freshwater Creek Slough to document its use by juvenile salmonids. NSA also began sampling Elk River Slough and Salmon Creek estuary to determine if juvenile salmonids also rear in the tidal portions of these large Humboldt Bay tributaries. NSA also conducted some qualitative sampling of Martin Slough. Then beginning in 2007 NSA began sampling smaller Humboldt Bay tributaries such as Rocky Gulch, and Wood Creek to determine if juvenile salmonids use these very small estuaries as rearing habitat or if they offer over wintering habitat during high stream flow events. By describing life history traits and habitat needs of juvenile coho salmon, Chinook salmon, steelhead trout, and sea-run coastal cutthroat trout this project hopes to provide important data to the restoration community to help restoration planning projects succeed. This project will provide “snapshots” of juvenile salmonid use of these areas before and after restoration projects.

Field Note December 18, 2008 Non-native Sacramento pikeminnow (Ptychocheilus grandis) Investigation Humboldt Bay tributary: Martin Slough November 2008

Tue, 15 Jun 2010 08:33:29 -0700

Sacramento pikeminnow surveys and eradication effort - On August 7, 2008, Martin Slough was the site of the first documented observation of Sacramento pikeminnow in any Humboldt Bay tributary. From August-October 2008, CDFG conducted numerous pikeminnow sampling trips in Martin Slough and Creek and the Elk River/Slough watershed and found no additional pikeminnow (CDFG October 30, 2008 Field Note). However, on November 6, 2008 during their regularly scheduled monthly sampling for juvenile salmonids, NSAP captured two more pikeminnow in Martin Slough. Following the capture of these two additional pikeminnow, CDFG organized two intensive pikeminnow sampling efforts on November 10 and 19. This field note summarizes the results of the continued CDFG Sacramento pikeminnow eradication sampling efforts in Martin Slough, a tributary to Swain Slough, thence Elk River, thence Humboldt Bay.