A Framework for Research Addressing the Role of Ammonia/Ammonium in the Sacramento-San Joaquin Delta and the San Francisco Bay Estuary Ecosystem

CALFED | April 13th, 2009

The Sacramento-San Joaquin Delta and the San Francisco Bay Estuary ecosystem has been drastically altered by human activity since at least the mid-1800s, leading to numer

The Sacramento-San Joaquin Delta and the San Francisco Bay Estuary ecosystem has been drastically altered by human activity since at least the mid-1800s, leading to numerous physical, chemical and biological changes [e.g., see Healey (2008) and Healey et al. (2008) for overviews]. Recent concerns include (1) the precipitous decline of four fish species that inhabit the Delta (collectively referred to as the pelagic organism decline, or POD) and (2) apparent major shifts in community composition of algae and higher trophic levels in the Delta and downstream in Suisun Bay. The four POD species of concern are delta smelt (longfin smelt), threadfin shad and striped bass. One of the potential causes of the POD and the community changes is the discharge of increasing concentrations of a combination of ammonia (NH3) and ammonium (NH4+) into the Delta ecosystem and eventually into Suisun Bay. For brevity, we hereafter abbreviate the ammonia/ammonium combination as ammonia/um. To address the potential for adverse effects of ammonia/um on the Bay-Delta ecosystem, a ammonia/um workshop was convened by the CALFED Science Program on 10 and 11 March 2009 in Sacramento, California. We participated as an expert panel and were charged with preparing a framework for research that will address the role of ammonia/um in the Bay-Delta ecosystem. In this report, we present our perception and interpretation of the major concerns related to ammonia/um in the Bay-Delta ecosystem; a conceptual framework of the major physical, chemical and biological drivers controlling the ecosystem (including POD populations); our assessment of the major research needs; and concluding remarks. For some research needs, we recommend specific types of research and provide literature citations; however, for other research needs we recommend general approaches for which targeted research will be determined later. In many ways, Bay-Delta research is breaking new ground by tackling a large-scale, complex freshwater-estuarine ecosystem affected by multiple, interactive stressors. Consequently, the Bay-Delta research program will establish a template for future research and management decisions in other hydrologically, biogeochemically, and trophically-similar systems, rather than relying on paths trodden by others.

A Machine Learning Tool for Design of Behavioral Fish Barriers in the Sacramento-San Joaquin River Delta

U.S. Geological Survey (USGS) | January 16th, 2024

Survival of out-migrating juvenile salmonids (Oncorhynchus spp.) through the Sacramento-San Joaquin River Delta averages less than 33 percent, depending on water flow thr

Survival of out-migrating juvenile salmonids (Oncorhynchus spp.) through the Sacramento-San Joaquin River Delta averages less than 33 percent, depending on water flow through the delta, and is partially governed by the distribution of fish among three Sacramento River distributaries: Sutter, Steamboat, and Georgiana sloughs. Behavioral altering structures in the junctions of the distributaries can effectively increase entrainment into favorable routes, thereby increasing through-delta (Verona to Chips Island, California) survival. The effectiveness of these structures, hence forth called “behavioral barriers,” are dependent on shape, length, location, barrier type, and water velocity, which is governed by Sacramento River discharge (hereinafter referred to as “flow”).

A New Approach to Accounting for Environmental Water Insights from the Sacramento–San Joaquin Delta

Public Policy Institute of California (PPIC) | November 9th, 2017

How water is apportioned to California’s cities, farms, and the environment can lead to conflict and competition in times of drought. Allocation of water to the environ

How water is apportioned to California’s cities, farms, and the environment can lead to conflict and competition in times of drought. Allocation of water to the environment in particular is poorly accounted for and poorly understood—shortcomings that can affect water policy, decision making, and public perception. This report reviews the state’s long-standing methods for defining and accounting for environmental water and proposes reforms to improve the timeliness, transparency, and detail in the accounting of environmental water allocation.

A Preliminary Study of the Effects of Water Circulation in the San Francisco Bay Estuary

U.S. Geological Survey (USGS) | July 15th, 1970

A Rapid Assessment Method to Identify Potential Groundwater Flooding Hotspots as Sea Levels Rise in Coastal Cities

Water, Multidisciplinary Digital Publishing Institute (MDPI) | October 25th, 2019

Sea level rise (SLR) will cause shallow unconfined coastal aquifers to rise. Rising groundwater can emerge as surface flooding and impact buried infrastructure, soil beh

Sea level rise (SLR) will cause shallow unconfined coastal aquifers to rise. Rising groundwater can emerge as surface flooding and impact buried infrastructure, soil behavior, human health, and nearshore ecosystems. Higher groundwater can also reduce infiltration rates for stormwater, adding to surface flooding problems. Levees and seawalls may not prevent these impacts. Pumping may accelerate land subsidence rates, thereby exacerbating flooding problems associated with SLR. Public agencies at all jurisdiction levels will need information regarding where groundwater impacts are likely to occur for development and infrastructure planning, as extreme precipitation events combine with SLR to drive more frequent flooding. We used empirical depth-to-water data and a digital elevation model of the San Francisco Bay Area to construct an interpolated surface of estimated minimum depth-to-water for 489 square kilometers along the San Francisco Bay shoreline. This rapid assessment approach identified key locations where more rigorous data collection and dynamic modeling is needed to identify risks and prevent impacts to health, buildings, and infrastructure, and develop adaptation strategies for SLR.

A Review of Delta Fish Population Losses from Pumping Operations in the Sacramento-San Joaquin River Delta

Sacramento Regional County Sanitation District (RegionalSan) | January 30th, 2010

To reduce fish loss at the pumps, the state and federal water export facilities operate facilities which are designed to salvage fish from the water and return them to th

To reduce fish loss at the pumps, the state and federal water export facilities operate facilities which are designed to salvage fish from the water and return them to the Delta. Fish facilities include the SWP Skinner Fish Protection Facility and CVP Tracy Fish Collection Facility. The fish facilities utilize two sets of louvers to prevent fish from entering further into water project operations and ultimately the powerful pumps. The louvers concentrate fish so that they can be removed prior to the water diversions. However, these fish salvage operations are inefficient, as high numbers of fish are lost due to predation in the waterways leading to the fish facilities, and the louvers are inefficient.

A Review of the Use of Science and Adaptive Management in California’s Draft Bay Delta Conservation Plan

National Academy of Sciences (NAS) | May 5th, 2011

California’s draft Bay Delta Conservation Plan—a draft plan to conserve habitat for endangered and threatened species, while continuing to divert water to agriculture

California’s draft Bay Delta Conservation Plan—a draft plan to conserve habitat for endangered and threatened species, while continuing to divert water to agriculture and domestic water users in central and southern California—is incomplete and contains critical scientific gaps. The Bay Delta is a large, complex ecosystem that supplies water from the state’s wetter northern regions to the drier southern regions, and also serves as habitat for many species. The Bay Delta Conservation Plan describes a proposal to construct a tunnel or canal to divert water from the northern Delta to the south, thus reducing the need to convey water through the Delta. This report reviews the use of science and adaptive management in the draft Bay Delta Conservation Plan and identifies opportunities to develop a more successful plan.

A Spatiotemporal History of Key Pelagic Fish Species in the San Francisco Estuary, CA

Springer | April 11th, 2023

A Study of Economic and Financial Policies for State Water Projects

State of California | August 5th, 1959

A Summary of Water-Quality Monitoring in San Francisco Bay in Water Year 2017

U.S. Geological Survey (USGS) | July 1st, 2020

This report summarizes the activities of the U.S. Geological Survey (USGS) San Francisco Bay Water-Quality Monitoring and Sediment Transport Project during water

This report summarizes the activities of the U.S. Geological Survey (USGS) San Francisco Bay Water-Quality Monitoring and Sediment Transport Project during water year 2017, including an explanation of methods employed, stations operated, and a graphical summary of data for the period of record for stations operational in water year 2017. In cooperation with partner agencies, the USGS maintains a network of sensors that continuously and autonomously measures water-quality parameters in San Francisco Bay including water temperature, specific conductance, turbidity, and suspended-sediment concentration. Data are collected at several locations in the estuary by a network of water-quality sondes sampled at 15-minute intervals. Methods of data collection are presented along with documentation of the regression models utilized to estimate suspended-sediment concentration from observed turbidity, a commonly utilized surrogate to estimate suspended-sediment concentration. The goals of the data collection effort are to (1) obtain long-term, high-frequency, and high-quality data to describe San Francisco Bay water quality; (2) make the data publicly available on the USGS National Water Information System data portal; and (3) help improve understanding of the spatial and temporal variability of water quality in the estuary, informing management decisions regarding restoration, water supply, navigation, and ecology.