Fish catch, invertebrate catch, and water quality data from the Sacramento-San Joaquin Delta collected by the Fish Restoration Monitoring Program, 2015-2017. The Fish Restoration Program Monitoring Team is tasked with monitoring fish and food web resources in restored tidal wetland sites. These restored sites are located in the Sacramento-San Joaquin Delta and Suisun Marsh pursuant to requirements in the 2008/2009 Biological Opinions for state and federal water project operations. Data on fish and invertebrate abundance on or near these sites was collected as baseline monitoring data and to determine the most efficient methods for monitoring wetlands.

The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. EDSM focuses on providing real-time data to help managers respond to population patterns of Delta Smelt within the upper San Francisco Estuary, primarily by providing estimates of Delta Smelt distribution and abundance. The dataset can also be useful in evaluating habitat use and behavior patterns of this species and other fish species of interest. Sampling is done year round via Kodiak trawls and larval (“20-mm”) gear to sample Delta Smelt across most life stages. Sites are chosen via stratified random sampling. Over the course of a week, field crews sample between 18 and 41 random sites. A minimum of two tows are conducted at each site. All fish collected are identified (in the field when possible, in the lab for early life stages), measured, enumerated, and recorded. In addition to fish information, environmental data are collected for each sampling event. For more information: https://www.fws.gov/project/enhanced-delta-smelt-monitoring-program

Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. The YBFMP operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. Only juvenile and adult fish catch with associated water quality are presented in this dataset. The rotary screw trap sampling objectives are to: (1) examine species abundance and life stage of juvenile outmigrants and resident small-bodied fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, and (3) examine the effect of physical and environmental conditions on these patterns. The fyke trap sampling objectives are to: (1) examine abundance of migrating and resident adult fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, especially with regard to anadromous species, (3) examine the effect of physical and environmental conditions on these patterns, and (4) provide data on the timing and duration of species captured in the Yolo Bypass for comparison to those captured in other Sacramento Valley tributaries. The beach seine surveys are conducted in the Yolo Bypass’s perennial channel (Toe Drain), inundated floodplain, disconnected inundated ponds, and perennial ponds. The objectives of Toe Drain and inundated floodplain beach seine sampling are: (1) to examine species abundance and composition in different water year types and inundation conditions, (2) to spatially compare fish abundance and diversity in the Yolo Bypass, and (3) to estimate growth rates and densities of salmon in the Yolo Bypass versus the Sacramento River. The objectives for beach seine sampling in disconnected inundated ponds are: (1) measure the diversity and abundance of fish species stranded in ponds located in different regions and habitats, (2) to compare relative densities of fish before and after floodplain drainage, (3) to examine the sources of fish mortality in ponds including temperature, desiccation and predation, (4) to develop long-term annual Yolo Bypass stranding indices for reference locations, and (5) to examine relationships between annual stranding indices and physical variables such as hydrology and temperature. The objectives for seine sampling in the perennial ponds are: (1) to examine seasonal fish species abundance and diversity in the Yolo Bypass versus the Sacramento River and (2) to examine species abundance and composition in different water year types. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Key

Overview The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work and associated monitoring in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains three datasets for adult White Sturgeon (Acipenser transmontanus) monitoring in the San Joaquin River (SJR) conducted by the US Fish and Wildlife Service, Lodi Fish and Wildlife Office. The primary purpose for this sampling was to capture White Sturgeon and implant acoustic telemetry tags for a tracking project. Therefore, the data are useful for determining when and where White Sturgeon were captured, but they should not be used to determine actual distribution or abundance. SJR_Adult_WST_Set contains data from a sampling program using various methods to catch adult White Sturgeon in the San Joaquin River. Sets were made at targeted locations primarily from March-May in 2012-2018 (other dates were occasionally sampled). SJR_Adult_WST_Catch contains data for individual fish caught via gillnets, trammel nets, setlines, or angling in the San Joaquin River. Species and fork length were recorded for all fish. For White Sturgeon, girth, maturation, tag, and surgery information are provided. SJR_Fish_Taxonomy contains data for fish codes used in the Catch datafile. For each species that was captured, the Species codes are listed with the corresponding Interagency Ecological Program code, common name, taxonomy (Phylum, Class, Order, Family, Genus, and Species), and whether or not the species is native to the region.

Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. The YBFMP operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. Only juvenile and adult fish catch with associated water quality are presented in this dataset. The rotary screw trap sampling objectives are to: (1) examine species abundance and life stage of juvenile outmigrants and resident small-bodied fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, and (3) examine the effect of physical and environmental conditions on these patterns. The fyke trap sampling objectives are to: (1) examine abundance of migrating and resident adult fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, especially with regard to anadromous species, (3) examine the effect of physical and environmental conditions on these patterns, and (4) provide data on the timing and duration of species captured in the Yolo Bypass for comparison to those captured in other Sacramento Valley tributaries. The beach seine surveys are conducted in the Yolo Bypass’s perennial channel (Toe Drain), inundated floodplain, disconnected inundated ponds, and perennial ponds. The objectives of Toe Drain and inundated floodplain beach seine sampling are: (1) to examine species abundance and composition in different water year types and inundation conditions, (2) to spatially compare fish abundance and diversity in the Yolo Bypass, and (3) to estimate growth rates and densities of salmon in the Yolo Bypass versus the Sacramento River. The objectives for beach seine sampling in disconnected inundated ponds are: (1) measure the diversity and abundance of fish species stranded in ponds located in different regions and habitats, (2) to compare relative densities of fish before and after floodplain drainage, (3) to examine the sources of fish mortality in ponds including temperature, desiccation and predation, (4) to develop long-term annual Yolo Bypass stranding indices for reference locations, and (5) to examine relationships between annual stranding indices and physical variables such as hydrology and temperature. The objectives for seine sampling in the perennial ponds are: (1) to examine seasonal fish species abundance and diversity in the Yolo Bypass versus the Sacramento River and (2) to examine species abundance and composition in different water year types. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Key

MESHR has been testing an approach focused on habitat metrics and fish response for determining effectiveness of large wood treatments. Data is collected using an adapted protocol from the Washington State Salmon Recovery Funding Board (Crawford 2011) and the U.S. Environmental Protection Agency (Kaufmann et al. 1999) to methodically measure habitat characteristics in stream reaches for a subsample of large wood installation projects using a Before-After, Control-Impact (BACI) study design. Large wood, residual water and pool depths, percent occurrence of particular substrates, substrate embeddedness, fish cover, and snorkel validation data are documented. 1.092 MB. This data and metadata were submitted by California Department of Fish and Wildlife (CDFW) Staff though the Data Management Plan (DMP) framework with the id: DMP000238. For more information, please visit https://wildlife.ca.gov/Data/Sci-Data.

The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work and associated monitoring in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains three datasets for juvenile White Sturgeon (Acipenser transmontanus) monitoring in the San Joaquin River (SJR) conducted by the US Fish and Wildlife Service, Lodi Fish and Wildlife Office. After two years of this experimental sampling program, it was discontinued due to low catches of White Sturgeon. SJR_Juvenile_WST_Set Data This dataset contains data on an experimental sampling program using trammel nets and setlines to catch juvenile White Sturgeon in the San Joaquin River. Sets were made at targeted locations from November-January in 2016 and 2017. One White Sturgeon (1000 mm fork length) was captured in a trammel net in 2016. SJR_Juvenile_WST_Catch Data This dataset contains data for individual fish caught in trammel nets or setlines in the San Joaquin River. Species and fork length were recorded for all fish. For White Sturgeon, girth, maturation, and tag information are provided. SJR_Fish_Taxonomy Data This dataset contains data for fish codes used in the Catch datafile. For each species that was captured, the Species codes are listed with the corresponding Interagency Ecological Program code, common name, taxonomy (Phylum, Class, Order, Family, Genus, and Species), and whether or not the species is native to the region.

Fish monitoirng in a newly created freshwater tidal wetland on Decker Island. The dataset includes beach seine and electrofishing fish catch and fork length data collected primarily from early spring through the fall. Fyke traps were used a couple of times experimentally. The project was required per conditions in a USACE 404 permit and USFWS and NMFS biological opinions. This data and metadata were submitted by California Department of Fish and Wildlife (CDFW) Staff though the Data Management Plan (DMP) framework with the id: DMP000385. For more information, please visit https://wildlife.ca.gov/Data/Sci-Data.

This data documents fish response to fish passage and instream habitat restoration treatments. Juvenile salmonid snorkel surveys are conducted pre-treatment and post-treatment. Pool dimensions (length and width), maximum residual pool depth, temperature, flow, and water quality data are also recorded. Minnow traps are deployed in the vicinity of restoration treatments when stream conditions or hazards prevent snorkel observations or where additional monitoring methods are deemed necessary to determine juvenile salmonid presence. Winter Salmonid spawner surveys of potential redds, adult spawners, and carcasses are also performed. Survey data includes a 0.038 MB Snorkel Survey database and a 0.043 MB Spawner Survey database. This data and metadata were submitted by California Department of Fish and Wildlife (CDFW) Staff though the Data Management Plan (DMP) framework with the id: DMP000237. For more information, please visit https://wildlife.ca.gov/Data/Sci-Data.

The United States Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook Salmon Oncorhynchus tshawytscha and other fish species within the San Francisco Estuary (Estuary) since 1976 using a combination of surface trawls and beach seines. Since 2000, three trawl sites and 58 beach seine sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin Rivers. As part of the Interagency Ecological Program (IEP) that manages the Estuary, the DJFMP has tracked the relative abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon of all races as they outmigrate through the Sacramento-San Joaquin Delta for over four decades. The data that DJFMP collected has been used not only to help inform the management of Chinook Salmon, but also to monitor the status of native species of interest such as the previously listed Sacramento Splittail Pogonichthys macrolepidotus and invasive species such as Mississippi Silverside Menidia beryllina and Largemouth Bass Micropterus salmoides.For more information: https://www.fws.gov/lodi/juvenile_fish_monitoring_program/