Sampling and Analysis Plan for Microplastic Monitoring in San Francisco Bay and Adjacent National Marine Sanctuaries

San Francisco Estuary Institute (SFEI) | May 31st, 2017

Plastic in the ocean, and more specifically microplastic (particles <5 mm), has been gaining global attention as a pervasive and preventable threat to the health of m

Plastic in the ocean, and more specifically microplastic (particles <5 mm), has been gaining global attention as a pervasive and preventable threat to the health of marine ecosystems. Microplastic is ingested by marine organisms (Wright et al. 2013), and may impact their physiological processes (von Moos et al. 2012; Cole et al. 2013, 2015; Rochman et al. 2013, 2014b; Wright et al. 2013; Watts et al. 2015; Lu et al. 2016; Sussarellu et al. 2016). Microplastic may also contain harmful chemicals such as flame retardants, plasticizers, or dyes (Browne et al. 2013; Fries et al. 2013; Rochman et al. 2013, 2014 a,b), and may provide a substrate for the adsorption of other harmful chemicals in the ocean, like PCBs and DDT (Teuten et al. 2007), which then may be transferred up the food chain (e.g., Farrell and Nelson 2013; Rochman et al. 2014a; Setala et al. 2014). Many scientific questions remain, however, and there is a need for research on the patterns of distribution and uptake of microplastic by organisms in their ocean ecosystems.

San Francisco Bay: A Freshwater Starved Estuary

Bay Institute | September 1st, 2016

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estu

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estuary, documents how the ecological health of San Francisco Bay and the nearby ocean is at high risk because large-scale water diversion in the Bay’s watershed severely limits the amount of fresh water that reaches the Bay and alters the timing of that flow. Inflow to the Bay from its Central Valley watershed now averages less than half of what it would be without diversions; in some years just one-third of the runoff makes it to the Bay. The result is a nearly permanent drought for the Bay’s fish, wildlife, and their habitats. This radical alteration creates severe consequences for the Bay and marine ecosystems – and Bay Area residents pay the price. The study shows how unsustainable diversion of the Bay’s freshwater inflow: Dramatically cuts production of fish and shrimp that are the food source for marine mammals, like Orca Whales, and birds; Allows pollutants to accumulate to dangerous levels and encourages blooms of toxic algae; Reduces sediment supply to Bay Area wetlands and beaches; Makes it easier for undesirable non-native species to successfully invade the Bay Estuary. The San Francisco Bay Estuary is created by the mixing of fresh water from the Central Valley’s rivers with salt water from the Pacific Ocean. Dramatically reducing the inflow of fresh water generates cascading effects in the Bay’s watershed, the Bay itself, and coastal ocean waters. The report’s major findings include: On average, since 1975 more than half (53%) of runoff from the Central Valley watershed has been diverted, stored, or exported before it can reach the Bay – and in many years two-thirds or more of the Bay’s inflow is captured; As a result of intensive water diversions, the Bay experiences catastrophically dry years almost half the time (only one “supercritically dry” year occurred naturally between 1975-2014, but the Bay experienced nineteen supercritical years during that period); Numerous unrelated fish species – from sharks to salmon, from sturgeon to smelt – show strong positive correlations with Bay Inflow; many of these species are now endangered, and even commercially viable fisheries are in decline; Predators that feed on flow-dependent fish and shrimp are feeling the pinch – for example, dwindling supplies of Central Valley Chinook salmon may restrict the recovery of the local Orca whale population; Blooms of toxic “algae” (cyanobacteria) are becoming more frequent, and other pollutants are becoming more concentrated, as a result of reductions in freshwater flows from the Bay’s watershed; Bay Area beaches and tidal wetlands are deprived of sediment that was once transported by high river flows. The study reports that local businesses are likely to suffer from the Bay’s continued decline, including those related to commercial fishing and tourism. As our Bay, beaches, wetlands, and fish and wildlife populations deteriorate, the quality of life for many Bay Area residents will also be severely – and perhaps permanently – damaged. The study identifies four important approaches to improving Bay inflows: Update the State’s 21 year old water quality standards for the Bay Estuary to ensure adequate inflow Require all those who divert water destined for the Bay, not just a subset, to contribute their fair share of fresh water to support benefits enjoyed by all Californians Invest in local water supplies around the state including conservation, and recycling, that can generate millions of acre-feet of water and reduce reliance on water diverted from the Estuary and its watershed Coordinate management of flows with wetland and beach restoration to more effectively protect shorelines The study was prepared for the San Francisco Estuary Partnership, a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary, which also provided the majority of funding for the project.

San Joaquin River Restoration Program

San Joaquin River Restoration Program | December 13th, 2007

San Luis National Wildlife Refuge Complex Final Comprehensive Conservation Plan and Environmental Assessment

U.S. Fish and Wildlife Service (FWS) | July 31st, 2024

This Comprehensive Conservation Plan (CCP) will guide the management of the Merced National Wildlife Refuge (NWR), San Luis NWR and Grasslands Wildlife Management Area (W

This Comprehensive Conservation Plan (CCP) will guide the management of the Merced National Wildlife Refuge (NWR), San Luis NWR and Grasslands Wildlife Management Area (WMA) for the next 15 years. Located in Merced County, California (Figure 1-1), these three units are managed and administered by the San Luis National Wildlife Refuge Complex (the Complex). A fourth unit, the San Joaquin River NWR, is also managed and administered by the Complex but already has a CCP for its management, which was completed in 2006 and amended in 2022. For the sake of this document, the term Complex refers to the San Luis NWR, Merced NWR and Grasslands WMA only. The Complex comprises just four of the 568 refuges that currently make up the U.S. Fish and Wildlife Service (USFWS or the Service) National Wildlife Refuge System (NWRS or Refuge System). The mission of the NWRS is to conserve a network of lands and water for the conservation and management of fish, wildlife and plant resources of the United States for the benefit of present and future generations. As part of the Refuge System, the three units—Merced NWR, San Luis NWR and Grasslands WMA—addressed in this CCP provide important habitat for a unique assemblage of both wetland- (particularly waterfowl and other waterbirds) and upland-dependent wildlife species of California’s Central Valley. This CCP is divided into five chapters: Chapter 1, Introduction and Background; Chapter 2, Comprehensive Conservation Planning Process; Chapter 3, Refuge Resources; Chapter 4, Refuge Management Direction; and Chapter 5, Implementation. Click here for full appendices.

San Luis Obispo Coastkeeper v. Santa Maria Valley Water Conservation District

United States District Court, Central District of California | September 23rd, 2022

Scott Valley Integrated Hydrologic Model: Data Collection, Analysis, and Water Budget Final Report

University of California, Davis (UC Davis) | November 14th, 2017

The Scott Valley is an agricultural groundwater basin in Northern California, within the Scott River watershed and part of the much larger Klamath Basin watershed straddl

The Scott Valley is an agricultural groundwater basin in Northern California, within the Scott River watershed and part of the much larger Klamath Basin watershed straddling the California-Oregon border. The Scott River provides important habitat for salmonid fish, including spawning and rearing habitat for coho and fall-run Chinook salmon and steelhead trout. Sufficient flows at adequately low temperatures during summer, for rearing, and fall, for spawning, are critical for healthy fish habitat in the mainstem and tributaries. This report presents the data assembled and the methods used for data analysis and data modeling to prepare the Scott Valley Integrated Hydrologic Model Version 2, which is currently under development. The report includes precipitation data analysis, streamflow data analysis and modeling, geology and groundwater data review and analysis, evapotranspiration and soils data analysis, and preparation of relevant watershed, land use, topography, and irrigation data. The data collection and analysis efforts culminate in the development of a spatio-temporally distributed soil water budget model for the Scott Valley. The soil water budget model is used to determine spatially and temporally varying groundwater pumping rates, surface water diversion rates, and groundwater recharge across the groundwater basin. The spatial resolution of the soil water budget model is by individual fields (land use polygons). Temporal discretization is in daily time steps for the period from October 1, 1990 to September 30, 2011. This period includes several dry years, average years, and wet year periods. Methods and results of the soil water budget model are presented in this report. This report represents the next step toward a better understanding of the interactions between groundwater, surface water, land-use, and agricultural practices with a specific focus on the seasonal impacts of groundwater pumping on streamflow during critical low flow periods. The work presented here relies on an extensive data collection facilitated by the voluntary and active collaboration of communities, landowners, the Scott River Watershed Council (SRWC), the Siskiyou Resource Conservation District (SRCD), and the Scott Valley Groundwater Advisory Committee (GWAC) which has been appointed by the Board of Supervisors in January 2011, meeting monthly since April 2011 and advising UC Davis on its data collection and modeling efforts. In the data analysis and during the model development, numerous assumptions have been made as is common in building a conceptual and numerical integrated hydrologic model. Models cannot represent the complexity of the real system, but are an effort to capture salient hydrologic features with sufficient accuracy to develop modeling results that are useful for a better understanding of the watershed dynamics and water balance.

Sediment Mobility and River Corridor Assessment for a 140-Kilometer Segment of the Main-Stem Klamath River Below Iron Gate Dam, California

U.S. Geological Survey (USGS) | January 26th, 2021

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California. Field and remote sensing methods were used to assess fundamental indicators of active sediment transport and river response to a combination of natural runoff events and reservoir releases during the study period from 2005 to 2019. Discharge measurements at two gaged sites and bed-material samples at two ungaged sites provided direct and indirect evidence of mobile bed conditions, scour and fill, and surface flushing of fine sediment. Available remote-sensing datasets collected in 2005, 2009, 2010, and 2016 were used to determine sediment storage, flood inundation boundaries, and provide indirect evidence of flood-induced scour. These datasets validate channel-maintenance flows defined by Shea and others (2016). During the study period, flows greater than or equal to 6,030 cubic feet per second mobilized the substrate, caused localized scour, and flushed fine sediment from bar surfaces. Flows greater than or equal to 10,400 cubic feet per second stripped vegetation from bars and floodplains and produced deeper scour. Flood disturbance within the study reach is produced by the combined effect of natural flows and reservoir releases, which resulted in mobile bed conditions during the study period. Periodic scour and substrate disturbance are considered by the U.S. Fish and Wildlife Service to be integral for managing disease-induced mortality of juvenile and adult salmonids. Substrate conditions conducive to parasites that host infectious diseases, particularly Ceratonova shasta, occur periodically. Additional studies are required to determine whether disease prevalence can be mitigated by well-timed reservoir releases. Study results are useful for interpreting linkages among physical and biological processes and for evaluating the effectiveness of flow management targeted to improve river bed conditions for endangered salmonid populations.

Sediment Transport in Two Tributaries to the San Joaquin River Immediately Below Friant Dam—Cottonwood Creek and Little Dry Creek, California

U.S. Geological Survey (USGS) | May 2nd, 2023

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow dynamics between October 1, 2011, and September 30, 2019. The two systems deliver sediment to the San Joaquin River below Friant Dam, California. Dams create downstream discontinuities in streamflow and sediment transport and therefore influence fish habitat and sediment dynamics. Because these two creeks are directly downriver from Friant Dam, they become the most upstream source of sediment to the San Joaquin River below Friant Dam. The quality and quantity of spawning habitat for fish in the gravel-bedded reach of the San Joaquin River relies on a range of bed material particle size suitable for redd structure. The effects of coarse-sand to fine-gravel supply on salmonid habitat depends primarily on the size of the sediment and the timing of its addition from tributaries to the San Joaquin River; thus, understanding the timing, quantity, and size of sediment supplied from these two tributaries is critical to the management of ecological and biological sustainability. Streamflow from Cottonwood and Little Dry Creeks, along with streamflow from the San Joaquin River below Friant Dam, were compared to continuously measured water-surface elevations to quantify the timing and direction of streamflow. Suspended-sediment samples were collected with multiple automatic samplers and analyzed for concentration and grain-size distribution. Measured suspended-sediment concentrations and streamflows were used to develop sediment rating curves and compute continuous estimates of suspended-sediment load for each tributary. Satellite imagery was used to qualify spatial and temporal dynamics through the lower watersheds and support more quantitative sediment-load estimates. Computed annual sediment loads ranged from 1.32x101 to 2.68x104 metric tons for Little Dry Creek and 9.82 to 1.98x103 metric tons for Cottonwood Creek. Sediment loads computed during the study period for both watersheds show that annual loads were highest during water year 2017 (October 1, 2016, to September 30, 2017). Sediment transport primarily occurred between the months of January and March. In both tributaries, grain-size distributions of suspended sediment were predominantly coarse-sized sand and were finer than the remnant bed material. Both creeks demonstrate backwater effects from the San Joaquin River, but the more tortuous stream channel and historical mining pits within Little Dry Creek provide more capacity for sediment storage compared to the less complex stream network of Cottonwood Creek. Because loads were computed based on upstream streamgages and not at the confluence of each tributary to the San Joaquin River, annual load estimates do not represent direct flux into the San Joaquin River; instead, these results indicated that in Little Dry Creek, particularly, the lowest portion of the watershed stores sediment before it reaches the San Joaquin River.

Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017

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

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) muscle tissues collected from live sturgeon

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) muscle tissues collected from live sturgeon during the California Department of Fish and Wildlife’s fall sturgeon tagging studies in North San Francisco Bay. The goal of this study was to non-lethally collect a large number of sturgeon muscle plugs and analyze them for selenium to (1) establish an understanding of current status, trends, and causes of variability in sturgeon muscle selenium concentrations; and (2) evaluate the potential for long-term sturgeon selenium monitoring with muscle plugs, through development of field and laboratory methods and informing the monitoring design. Monitoring of selenium in white sturgeon is needed to evaluate the effectiveness of the North Bay Selenium Total Maximum Daily Load (TMDL) in protecting sturgeon from selenium toxicity. This technical report provides documentation of the study and presents its major findings in the context of all historically available data on sturgeon muscle selenium concentrations in San Francisco Bay. 

Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study

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

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturg

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturgeon Derby events in North San Francisco Bay. The goal of this study was to investigate the distribution of selenium among sturgeon tissues to inform the toxicological and regulatory interpretation of selenium measured in non-lethally collected tissues, including muscle plugs and fin rays. This technical report provides documentation of the study and presents its major findings.