“Where Have All The Fish Gone? Interactive Factors Producing Fish Declines in the Sacramento-San Joaquin Estuary

American Association for the Advancement of Science (AAAS) | June 19th, 1994

2014 Clear Creek Technical Team Report for the Coordinated Long-Term Operation Biological Opinions Integrated Annual Review October 3, 2014

Delta Stewardship Council (Delta Council) | October 3rd, 2014

2015 Annual Monitoring Report

San Francisco Estuary Institute (SFEI) | July 1st, 2016

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is the primary source for long-term contaminant monitoring information for the San Francisco

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is the primary source for long-term contaminant monitoring information for the San Francisco Bay. The RMP is an innovative and collaborative effort among the scientific community, the San Francisco Bay Regional Water Quality Control Board (Water Board), and the regulated discharger community. The Program was initiated by the Water Board as a pilot study in 1989 and has been collecting water, sediment, and bivalve tissue data since its official inception in 1993. Regular monitoring of sport fish tissue and bird eggs for toxic contaminants was incorporated into the Program in 1997 and 2006, respectively. The Program monitors the different matrices included in “status and trends” monitoring on varying schedules. Additional monitoring occurs as part of short-term “special studies” or pilot studies focused on new regions, matrices, or contaminants of immediate or increasing regulatory interest. In 2015, the RMP collected only water data as part of “status and trends” monitoring. A pilot study was also conducted to collect sediment data from the Bay margins. Bird egg monitoring was originally scheduled to be conducted in 2015, but was delayed until 2016. The purpose of this report is to document RMP monitoring activities in 2015. The report is organized into chapters on water and sediment. Each chapter contains information on: • The locations where these samples were collected, • The field sampling methods, • The target analytes, laboratories, and analytical methods for each matrix, and • Any problems encountered or non-conformances to planned procedures.

2015 Technical Memorandum Regarding the Accounting of San Joaquin River Spring-run Chinook Salmon at the Central Valley Project and State Water Project Sacramento-San Joaquin Delta Fish Collection Facilities

National Marine Fisheries Service (NMFS) | January 15th, 2015

2016 Regional Monitoring Program (RMP) Sturgeon Derby Study Sampling & Analysis Plan

San Francisco Estuary Institute (SFEI) | February 1st, 2016

A second year of Sturgeon Derby monitoring will be conducted in collaboration with the 32nd annual Original Sturgeon Derby held by the Foundation Sportsman’s Club out

A second year of Sturgeon Derby monitoring will be conducted in collaboration with the 32nd annual Original Sturgeon Derby held by the Foundation Sportsman’s Club out of Bay Point, CA. The sturgeon derby and tissue sampling will occur on February 67, 2016. Tissue samples from female white sturgeon will be collected, and samples from up to fifteen sturgeon will be analyzed. The Derby offers an opportunity to collect a variety of tissue samples from fish caught for the competition that are otherwise unavailable. This will allow for comparison between selenium concentrations measured in tissues that are easy to obtain nonlethally (muscle plugs, fin rays) and those that are not, but may be of greater interest toxicologically (ovaries, liver) or analyzed for microchemistry (otoliths, for comparison with fin rays). If approved, additional collection of muscle fillet samples will also contribute to a better understanding of the relationship between muscle fillet and muscle plug selenium concentrations. Analysis of tissue samples for stable isotopes will also provide information on diet and habitat use by the sturgeon. Otolith microchemistry will be conducted to support development of a method for fin rays, which can be collected from sturgeon nonlethally during future monitoring efforts. This study will be performed as a collaboration between SFEI (with RMP funding), USFWS, USGS, UC Davis, and Stantec. The purpose of this Sampling and Analysis Plan is to outline the details for how the samples will be collected, handled, and analyzed by the various parties involved with the study. Additional pathology samples taken by USFWS will not be included in this document, except where needed to inform the collection of other samples.

2017 Margins Microplastics Cruise Report

San Francisco Estuary Institute (SFEI) | October 2nd, 2017

This report contains information on the summer field sampling efforts conducted by Coastal Conservation & Research (CC&R) in support of two Regional Monitoring Pr

This report contains information on the summer field sampling efforts conducted by Coastal Conservation & Research (CC&R) in support of two Regional Monitoring Program (RMP) studies: South Bay Margins and Moore Microplastics. The South Bay Margins is the second round of a larger San Francisco Bay study collecting sediment and water in shallow margin areas of the bay. The first round was conducted in Central Bay in 2015. The Moore Microplastics study is a collaborative effort with the Moore Foundation to collect sediment and fish samples in San Francisco and Tomales Bays. The work for both studies was contracted through the San Francisco Estuary Institute (SFEI) to CC&R. Since overall project management and sampling locations were coordinated between the two projects, activities from both studies will be presented as they occurred. 

2017/2018 Salmonid and Green Sturgeon Incidental Take and Monitoring Report

California Department of Water Resources (DWR) | October 19th, 2018

2019 Regional Monitoring Plan (RMP) North Bay Selenium Monitoring Sampling and Analysis Plan

San Francisco Estuary Institute (SFEI) | January 31st, 2020

In 2016, the State Water Resources Control Board approved a selenium TMDL for North San Francisco Bay. The TMDL established a target concentration of 11.3 ug/g dw in whi

In 2016, the State Water Resources Control Board approved a selenium TMDL for North San Francisco Bay. The TMDL established a target concentration of 11.3 ug/g dw in white sturgeon muscle tissue as the basis for evaluating impairment (SFBRWQCB 2015). Following discussions surrounding the North Bay TMDL, the San Francisco Bay Regional Water Quality Control Board asked the RMP Selenium Workgroup to develop a robust monitoring design for North Bay. The goal of the monitoring is to identify leading indicators of change to allow prompt management response to signs of increasing impairment. At the 2016 technical workshop, participants reached a consensus that monitoring sturgeon, clams, and water are all needed to answer management questions. Recommendations for long-term monitoring of these three matrices are detailed in the North Bay Monitoring Design document (Grieb et al. 2018). The USGS conducted monthly clam monitoring at multiple locations in North Bay for over 20 years, but USGS funding for this work ended in 2016. In 2019, the RMP will resume clam monitoring following a modified monitoring design optimized for early detection of changes in selenium trends in clams. These efforts will continue the long-term monitoring of Potamocorbula amurensis. Grieb et al. (2018) also recommended monitoring dissolved and particulate selenium in the water column. Long-term monitoring of water and sturgeon tissue in North Bay will be added to the clam sampling to track interannual trends and changes in sources or environmental processes influencing food web selenium exposures in North Bay. Potamocorbula amurensis and water samples will be collected from two long-term USGS monitoring locations in northern San Francisco Bay. Samples will be collected and processed by SFEI and Applied Marine Sciences (AMS) aboard the R/V Questuary . Sampling will take place over six months each year in two key three-month periods: July-September and December-February. White sturgeon ( Acipenser transmontanus ) samples will be collected by DFW during their tagging efforts aboard the New Alosa . These efforts occur during DFW’s fall tagging cruises (Sept - Oct). Non-lethal muscle plug samples will be collected from the epaxial muscle of each fish, just in front of the dorsal fin (Figure 5). Brooks Applied Labs (BAL), CalTest Analytical Laboratory (CalTest), and the UC Davis Stable Isotope Lab will be the analytical partners for this work. Stable isotope analysis will be used to identify spatial and temporal relationships within a food web, as well as potential sources of selenium. BAL will analyze dissolved and particulate selenium in water; clams, and sturgeon samples; and CalTest will conduct ancillary analyses on dissolved water samples. The purpose of this Sampling and Analysis Plan is to clearly document the sampling design, methods, and responsibilities; and to facilitate coordination among project partners.

2019 Regional Monitoring Program (RMP) Sport Fish Monitoring Sampling and Analysis Plan

San Francisco Estuary Institute (SFEI) | December 1st, 2019

2019 Technical Memorandum Regarding the Accounting of San Joaquin River Spring-run Chinook Salmon at the Central Valley Project and State Water Project Sacramento-San Joaquin Delta Fish Collection Facilities

National Marine Fisheries Service (NMFS) | January 15th, 2019