Sacramento River

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 freshwater conservation blueprint for California: prioritizing watersheds for freshwater biodiversity

Society for Freshwater Science | April 18th, 2018

Conservation scientists have adapted conservation planning principles designed for protection of habi- tats ranging from terrestrial to freshwater ecosystems. We

Conservation scientists have adapted conservation planning principles designed for protection of habi- tats ranging from terrestrial to freshwater ecosystems. We applied current approaches in conservation planning to prioritize California watersheds for management of biodiversity. For all watersheds, we compiled data on the pre- sence/absence of herpetofauna and fishes; observations of freshwater-dependent mammals, selected invertebrates, and plants; maps of freshwater habitat types; measures of habitat condition and vulnerability; and current manage- ment status. We analyzed species-distribution data to identify areas of high freshwater conservation value that op- timized representation of target taxa on the landscape and leveraged existing protected areas. The resulting priority network encompasses 34% of the area of California and includes ≥10% of the geographic range for all target taxa. High-value watersheds supported nontarget freshwater taxa and habitats, and focusing on target taxa may provide broad conservation value. Most of the priority conservation network occurs on public lands (69% by area), and 46% overlaps with protected areas already managed for biodiversity. A significant proportion of the network area is on private land and underscores the value of programs that incentivize landowners to manage freshwater species and habitats. The priority conservation areas encompass more freshwater habitats/ha than existing protected areas. Land use (agriculture and urbanization), altered fire regimes, nonnative fish communities, and flow impairment are the most important threats to freshwater habitat in the priority network, whereas factors associated with changing climate are the key drivers of habitat vulnerability. Our study is a guide to a comprehensive approach to freshwater conservation currently lacking in California. Conservation resources are often limited, so prioritiza- tion tools are valuable assets to land and water managers.

A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications

River Research and Applications (Wiley) | January 8th, 2020

A hybrid machine learning model to predict and visualize nitrate concentration throughout the Central Valley aquifer, California, USA

Science of the Total Environment (Elsevier) | June 9th, 2017

Intense demand for water in the Central Valley of California and related increases in groundwater nitrate concentration threaten the sustainability of the groundwater res

Intense demand for water in the Central Valley of California and related increases in groundwater nitrate concentration threaten the sustainability of the groundwater resource. To assess contamination risk in the region, we developed a hybrid, non-linear, machine learning model within a statistical learning framework to predict nitrate contamination of groundwater to depths of approximately 500m below ground surface. A database of 145 predictor variables representing well characteristics, historical and current field and landscape-scale nitrogen mass balances, historical and current land use, oxidation/reduction conditions, groundwater flow, climate, soil characteristics, depth to groundwater, and groundwater age were assigned to over 6000 private supply and public supply wells measured previously for nitrate and located throughout the study area. The boosted regression tree (BRT) method was used to screen and rank variables to predict nitrate concentration at the depths of domestic and public well supplies. The novel approach included as predictor variables outputs from existing physically based models of the Central Valley. The top five most important predictor variables included two oxidation/reduction variables (probability of manganese concentration to exceed 50 ppb and probability of dissolved oxygen concentration to be below 0.5 ppm), field-scale adjusted unsaturated zone nitrogen input for the 1975 time period, average difference between precipitation and evapotranspiration during the years 1971–2000, and 1992 total landscape nitrogen input. Twenty-five variables were selected for the final model for log-transformed nitrate. In general, increasing probability of anoxic conditions and increasing precipitation relative to potential evapotranspiration had a corresponding decrease in nitrate concentration predictions. Conversely, increasing 1975 unsaturated zone nitrogen leaching flux and 1992 total landscape nitrogen input had an increasing relative impact on nitrate predictions. Three-dimensional visualization indicates that nitrate predictions depend on the probability of anoxic conditions and other factors, and that nitrate predictions generally decreased with increasing groundwater age.

A Machine Learning Approach to Predict Groundwater Levels in California Reveals Ecosystems at Risk

Frontiers in Earth Science (Frontiers) | December 17th, 2021

Groundwater dependent ecosystems (GDEs) are increasingly threatened worldwide, but the shallow groundwater resources that they are reliant upon are seldom monitored. In t

Groundwater dependent ecosystems (GDEs) are increasingly threatened worldwide, but the shallow groundwater resources that they are reliant upon are seldom monitored. In this study, we used satellite-based remote sensing to predict groundwater levels under groundwater dependent ecosystems across California, USA. Depth to groundwater was modelled for a 35-years period (1985–2019) within all groundwater dependent ecosystems across the state (n = 95,135). Our model was developed within Google Earth Engine using Landsat satellite imagery, climate data, and field-based groundwater data [n = 627 shallow (< 30 m) monitoring wells] as predictors in a Random Forest model. Our findings show that 1) 44% of groundwater dependent ecosystems have experienced a significant long-term (1985–2019) decline in groundwater levels compared to 28% with a significant increase; 2) groundwater level declines have intensified during the most recent two decades, with 39% of groundwater dependent ecosystems experiencing declines in the 2003–2019 period compared to 27% in the 1985–2002 period; and 3) groundwater declines are most prevalent within GDEs existing in areas of the state where sustainable groundwater management is absent. Our results indicate that declining shallow groundwater levels may be adversely impacting California’s groundwater dependent ecosystems. Particularly where groundwater levels have fallen beneath plant roots or streams thereby affecting key life processes, such as forest recruitment/succession, or hydrological processes, such as streamflow that affects aquatic habitat. In the absence of groundwater monitoring well data, our model and findings can be used to help state and local water agencies fill in data gaps of shallow groundwater conditions, evaluate potential effects on GDEs, and improve sustainable groundwater management policy in California.

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 multi-scale approach for identification of potential pesticide use sites impacting vernal pool critical habitat in California

Science of the Total Environment (Elsevier) | October 17th, 2022

Spatially explicit ecological risk assessment (ERA) requires estimating the overlap between chemical and receptor distribution to evaluate the potential impacts of exposu

Spatially explicit ecological risk assessment (ERA) requires estimating the overlap between chemical and receptor distribution to evaluate the potential impacts of exposure on nontarget organisms. Pesticide use estimation at field level is prone to error due to inconsistencies between ground-reporting and geospatial data coverage; attempts to rectify these inconsistencies have been limited in approach and rarely scaled to multiple crop types. We built upon a previously developed Bayesian approach to combine multiple crop types for a probabilistic determination of field-crop assignments and to examine co-occurrence of critical vernal pool habitats and bifenthrin application within a 5-county area in California (Madera, Merced, Sacramento, San Joaquin, and Stanislaus counties). We incorporated a multi-scale repeated sampling approach with an area constraint to improve the delineation of field boundaries and better capture variability in crop assignments and rotation schemes. After comparing the accuracy of the spatial probabilistic approach to USDA Census of Agriculture crop acreage data, we found our approach allows more specificity in the combination of crop types represented by the potential application area and improves acreage estimates when compared to traditional deterministic approaches. In addition, our multi-scale sampling scheme improved estimates of bifenthrin acreage variability for co-occurrence analysis and allowed for estimates of crop rotations that were previously uncaptured. Our approach could be leveraged for more realistic, spatially resolved exposure and effects models both in and outside of California.

A Path Forward for California’s Freshwater Ecosystems

Public Policy Institute of California (PPIC) | December 2nd, 2019

Californians rely on freshwater ecosystems for many things: water supply, hydropower, recreation, fisheries, flood risk reduction, biodiversity, and more. These ecosystem

Californians rely on freshwater ecosystems for many things: water supply, hydropower, recreation, fisheries, flood risk reduction, biodiversity, and more. These ecosystems—and the social, economic and environmental benefits they provide—are part of the state’s natural infrastructure. But they are changing in undesirable ways in response to water and land use, pollution, introduction of non-native species, and a changing climate. Declines in native biodiversity are the most direct measure of these changes, with numerous species now protected by state and federal endangered species acts (ESAs) and many times more likely to need protection in future.  For the past 40 years, the ESAs have played a prominent role in managing the state’s freshwater ecosystems. While this approach has prevented extinctions, it also places an emphasis on reducing harm to listed species, rather than improving overall ecosystem condition necessary to recover their populations. And these laws are not forward-looking enough to help species adapt to changing climate and reduce future species listings. This approach also fuels controversy and litigation due to perceptions about trade-offs between species protection and economic uses of land and water.  To maintain the benefits that Californians derive from their freshwater ecosystems—and arrest the decline of native biodiversity—a new approach is needed. We recommend that the state adopt the principles and practices of ecosystem-based management. This involves the simultaneous management of water, land, and organisms to achieve a desired ecosystem condition that benefits both native biodiversity and human well-being. The goal of ecosystem-based planning is to develop a shared vision for the ecosystem, agreement upon a common set of facts, and a unified plan to achieve it. We are not proposing major reforms to state or federal endangered species acts. Rather, we recommend a shift in the way these acts are implemented.  Ecosystem-based management relies on robust governance frameworks that are transparent, collaborative, and supported by science and secure funding. Many programs are starting to adopt its principles and practices, but much more needs to be done. Actions needed to achieve ecosystem-based objectives include setting aside water budgets for the environment and using this water to improve ecosystem condition and create multiple benefits. Binding comprehensive agreements between regulatory agencies, stakeholders, and water users—developed as part of sustainable watershed management plans—should guide implementation. These plans can be used to align agency actions and permitting and can be adopted by the State Water Board as water quality control plans.  California needs to change course in how it manages freshwater ecosystems to protect the many beneficial uses they provide. Ecosystem-based management offers a more comprehensive, flexible, and adaptive approach, and one that is compatible with existing laws. We believe this approach is better able to improve ecosystem outcomes that benefit both people and nature and respond to today’s challenges while preparing for an uncertain future. 

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

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

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.