Sustainable Water and Environmental Management in the California Bay-Delta

National Academy of Sciences (NAS) | March 29th, 2012

Water management in the California Bay Delta is directed toward providing a more reliable water supply for California, and protecting and rehabilitating the Delta eco

Water management in the California Bay Delta is directed toward providing a more reliable water supply for California, and protecting and rehabilitating the Delta ecosystem, including five endangered and threatened populations and species of fish that live in or migrate through the Delta. However, water management in the Bay and Delta is distributed among many agencies and organizations, a structure that hinders the development and implementation of an integrated, comprehensive plan. As a result, recent Bay Delta planning efforts have not resolved the best plan for the environment or for satisfying anticipated water needs. Challenges include the fact that water scarcity has not been adequately addressed in planning for Delta water and environmental management; the interacting effects of the many environmental stressors that impact the Delta ecosystem, and the many biological and physical effects of climate change. This report discusses the issue of scarcity, factors affecting the listed species and the Delta ecosystem in general, future water-supply and delivery options, scientific uncertainties, the degree of restoration likely to be attainable, and the need for comprehensive planning. Key Messages Planning efforts to implement the two goals of providing a more reliable water supply for California and protecting and rehabilitating the Delta ecosystem have not led to clarity on how the inevitable tradeoffs between the two goals should be managed, particularly when water is in short supply. Climate change is one of most challenging and important issues confronting the management and rehabilitation of the Delta ecosystem. Changes in climate are expected to have profound effects on the physical and ecological structure and functioning of the Delta, as well as on the availability of water in California. Many environmental stressors, including water diversions, contaminants in the water, and introduced species affect the structure and functioning of Delta ecosystems. Interactions among stressors and between stressors and ecosystem processes are widespread and complex. Furthermore, species differ in their responses to stress. This complicates the interpretation and evaluation of the effects of stressors on the ecosystem, and makes it impossible to identify which stressor is the root cause of a certain environmental problem, or even to rank the stressors with any certainty. The large number of stressors, their effects and interactions lead to the conclusion that efforts to eliminate any one stressor are unlikely to reverse declines in listed species. Opportunities exist to mitigate or reverse the effects of many stressors. Continued effects analyses, modeling, and monitoring are necessary to ensure actions taken to rehabilitate the ecosystem are cost-effective. Due to the extensive physical changes that have already taken place and are still occurring in the Delta ecosystem and its tributary watersheds, it will not be possible to restore the habitat to its pre-disturbance state. Delta restoration programs will need to balance consideration of an ecosystem approach with the Endangered Species Act's emphasis on individual species. Assessments suggest that many species will be affected by shifts changes in the pattern and type of precipitation due to climate change. Projected increases in mean sea level and extremes of precipitation have the potential to increase the frequency of levee failures and the inundation of islands, in part because the levees continue to subside due to the oxidation of peat. Sea level rise also has the potential to enhance salt water intrusion and alter water quality. Planning and evaluation of future environmental and economic scenarios will need to address uncertainties in projections, integrated analysis, and the development of risk management strategies. Future planning should also include a climate-change based risk model and analysis that incorporates data on the actual changes in Delta conditions as well as alternative future climate change scenarios and their probability. The instability of levees and the fact that the failure of one levee can affect others are likely to be major issues for achieving any measure of water-supply reliability or ecosystem rehabilitation. Continuing the status quo of improving levees will not always be the most environmentally sustainable or economically defensible response in the years ahead. Science is necessary to inform actions and proposals, but does not provide the entire, prioritized, integrated analysis needed. Societal and political considerations are also important factors in determining the most appropriate policy. Undertaking a comprehensive review of water planning and management functioning would allow California to anticipate future needs such as water scarcity, balanced consideration of all statewide water use practices, and water engineering alternatives. As a result, the Delta would be an effective partner in statewide water management plans. It is likely that the scarcity of water for all needs in the Delta will become severe. While more effective planning is developed, the state will need to use its water resources efficiently and productively. The committee has not analyzed the benefits and disadvantages of an isolated conveyance facility, because not enough specific information was available about it, and therefore there is no recommendation with respect to its adoption as a major part of water management in the Delta. However, the considerations such as the form such a facility would take, its size, location, and the diversion design and operation, including the role of current diversions, should be analyzed as part of any integrated Delta plan, and compared to alternative water management options, including current operations.

Sustainable Water Management Strategy for Specialty Crop Expansion in the Sacramento Valley

Sacramento Area Council of Governments (SACOG) | June 26th, 2018

The Sacramento Area Council of Governments (SACOG) is an association of local governments in the six-county Sacramento Region of El Dorado, Placer, Sacramento, Sutter, Yo

The Sacramento Area Council of Governments (SACOG) is an association of local governments in the six-county Sacramento Region of El Dorado, Placer, Sacramento, Sutter, Yolo, and Yuba counties (excluding the Tahoe Basin in Placer and El Dorado counties) and the 22 cities therein. SACOG provides planning and funding for the region and serves as a forum for the study and resolution of regional issues. SACOG prepares the region’s long range plan which considers both transportation and land use. Through the lens of rural planning, SACOG has actively engaged in a Rural-Urban Connections Strategy (RUCS) Program that has studied ways to enhance rural economies and natural assets. The RUCS Program includes a scenario analysis modeling tool that links a parcel-level crop map with environmental and economic factors, including a comprehensive profile of per acre operational cost and return metrics for each crop. The study described in this report looks at how new agricultural crops and markets coupled with improved irrigation techniques will support new specialty crop acreage in the SACOG area. While new and improved irrigation techniques can result in better crop yields and decreased water demands, increases in irrigation efficiency also result in reduced groundwater recharge from irrigation return flows. SACOG received grant funding from the California Department of Food and Agriculture (CDFA) to evaluate the feasibility of recharging groundwater on agricultural lands within the SACOG portion of the Sacramento Valley to benefit specialty crop production. The primary goal of the project is to bring together a broad range of different factors impacting groundwater recharge and infiltration and to identify areas across the region that are most suited for strategic flooding of specialty crop fields; in other words, areas that will most efficiently and effectively facilitate recharge, while minimizing cost to the specialty crop producer. Ultimately, this feasibility information will be incorporated into SACOG’s RUCS model to evaluate the potential benefits of recharging groundwater on agricultural land for the benefit of specialty crops.

Sutter County Groundwater Management Plan

Sutter County | March 19th, 2012

Sutter County intends this GMP to be relevant for the entire County. Sutter County overlies the south central part of the Sacramento Valley Groundwater Basin, and specif

Sutter County intends this GMP to be relevant for the entire County. Sutter County overlies the south central part of the Sacramento Valley Groundwater Basin, and specifically the Sutter Subbasin and portions of the East Butte and North American Subbasins. The majority of the County is serviced by water and irrigation districts, reclamation districts, cities, and public utility districts, which have the authority to manage groundwater in their service areas. Unless those entities decline to manage groundwater on their own, and instead enter into agreements with the County, this GMP does not formally apply to those areas. If those entities choose not to adopt their own GMPs, they have the option of taking formal action to adopt the Sutter County GMP for their areas. By doing so, they will fulfill the requirements of the groundwater management provisions of the California Water Code.

Synergies between climate anomalies and hydrological modifications facilitate estuarine biotic invasions

Ecology Letters (Wiley) | June 6th, 2011

Environmental perturbation, climate change and international commerce are important drivers for biological invasions. Climate anomalies can further increase levels of hab

Environmental perturbation, climate change and international commerce are important drivers for biological invasions. Climate anomalies can further increase levels of habitat disturbance and act synergistically to elevate invasion risk. Herein, we use a historical data set from the upper San Francisco Estuary to provide the first empirical evidence for facilitation of invasions by climate extremes. Invasive zooplankton species did not become established in this estuary until the 1970s when increasing propagule pressure from Asia coincided with extended drought periods. Hydrological management exacerbated the effects of post‐1960 droughts and reduced freshwater inflow even further, increasing drought severity and allowing unusually extreme salinity intrusions. Native zooplankton experienced unprecedented conditions of high salinity and intensified benthic grazing, and life history attributes of invasive zooplankton were advantageous enough during droughts to outcompete native species and colonise the system. Extreme climatic events can therefore act synergistically with environmental perturbation to facilitate the establishment of invasive species.

Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017

Interagency Ecological Program (IEP) | November 1st, 2021

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious managem

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the State of California. Early studies of Delta Smelt distribution within the SFE suggested that Delta Smelt habitat is determined largely by freshwater flow; however, the exact mechanisms and processes producing such benefits remained unclear. In the summer of 2017, the Flow Alteration Management, Analysis, and Synthesis Team (FLOAT-MAST) was established to analyze, synthesize, and summarize the data collected from the various flow-related monitoring and special studies occurring in 2017(see Table Intro 4). This report will focus on the 2017 summer-fall status of Delta Smelt and its habitat following a record wet year. There has been a long-term decline in the abundance of Delta Smelt associated with a decline in other pelagic fishes. Investigators concluded that the decline has likely been caused by the interactive effects of several causes, including changes in both physical and biotic habitats, many of which are tied to amount and timing of freshwater flow. For this report, we formulated a number of basic predictions about the likely effects of high flows in 2017 on Delta Smelt and their habitat (Table 3). We use a qualitative weight of evidence approach to evaluate whether these predictions were supported by available data. Data sources included a variety of long-term monitoring surveys conducted by Interagency Ecological Program (IEP) agencies, as well as model outputs. Delta Smelt population, health, and life history metrics rarely responded as predicted. Water temperature appears to have a stronger effect on Delta Smelt growth rate and some metrics of life history diversity than outflow or X2 position. Other life history diversity attributes varied but did not appear to be driven by outflow or temperature. Health status was difficult to interpret. Low prevalence of lesions and improved nutritional condition during the drought was contradicted by declining overall population levels. Because of the sparse catches of Delta Smelt in the post-POD years, we consider the data insufficient to reach firm conclusions about the predictions concerning range and distribution of Delta Smelt, especially in the fall. The prediction of high survival was not supported. The 2017 Delta Smelt year class began with poor recruitment in spring of 2017 and below average survival for spring to summer and summer to fall. Thus, low production and low survival led to low abundance of all life stages. During the fall to winter period survival improved, yet the resulting adults were low in number. Foraging success of the fish captured, as measured by stomach fullness, was high for juveniles and adults in 2017 relative to recent years associated with the higher densities of common zooplankton prey that occurred in 2017.

Synthesis of Data from High-Frequency Nutrient and Associated Biogeochemical Monitoring for the Sacramento– San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the second in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San J

This report is the second in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). The purpose of this report is to synthesize the data available from a nutrient and water-quality HF (about every 15 minutes) monitoring network operated by the U.S. Geological Survey in the northern Delta. In this report, we describe the network and focus on the purpose of each station. We then present and discuss the available data, at various timescales—first at the monthly, seasonal, and inter-annual timescales, and second, for comparison, at the tidal and event timescales. As expected, we determined that there is substantial variability in nitrate-N concentrations at short timescales within hours, but also significant variability at longer timescales such as months or years. Resolving this variability is made possible by the HF data, with the largest variability caused by storms, tides, and diel biological processes. Given this large temporal variability, calculations of cumulative nutrient fluxes (for example, daily, monthly, or annual loads) is difficult without HF data. For example, in the Cache Slough, calculation of the annual load without the tidal variability resulted in a 30 percent underestimation of the true annual load value. We conclude that HF measurements are important for accurate determination of fluxes and loads in tidal environments, but, more importantly, provide important insights into processes and rates of nutrient cycling. This report, along with the other two reports of this series (Bergamaschi and others, 2017; Kraus, Bergamaschi, and others, 2017), was drafted in cooperation with the Delta Regional Monitoring Program to help scientists, managers, and planners understand how HF data improve our understanding of nutrient sources and sinks, drivers, and effects in the Delta.

Technical Report on Barriers: A part of the comprehensive survey of San Francisco Bay and tributaries, California

U.S. Army Corps of Engineers (USACE) | March 15th, 1963

Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives

California State Water Resources Control Board (SWRCB) | February 15th, 2012

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay- Delta Plan). Figure 1.1 displays the project area corresponding to SJR flow objectives and program of implementation and Figure 1.2 displays the project area for the southern Delta water quality objectives and program of implementation. The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and their associated program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow objectives for the protection of fish and wildlife beneficial uses, southern Delta water quality objectives for the protection of agricultural beneficial uses, and the program of implementation contained in the 2006 Bay-Delta Plan. Also, the environmental impacts of these amendments will be evaluated in a Substitute Environmental Document (SED) in compliance with the California Environmental Quality Act. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.

Technical Review of the Draft Staff Report/Substitute Environmental Document in Support of Potential Updates to the Water Quality Control Plan and Associated Modeling

Northern California Water Association (NCWA) | January 18th, 2024

Technical Workshop on Estuarine Habitat in the Bay Delta Estuary

San Francisco Estuary Institute (SFEI) | March 27th, 2012

The Technical Workshop on Estuarine Habitat in the Bay Delta Estuary was initiated by U.S. Environmental Protection Agency (EPA), with support from the Aquatic

The Technical Workshop on Estuarine Habitat in the Bay Delta Estuary was initiated by U.S. Environmental Protection Agency (EPA), with support from the Aquatic Science Center (ASC), to obtain scientific input needed to inform EPA on California’s Comprehensive Review of the 2006 Water Quality Control Plan for the Bay Delta Estuary. Gathering a number of recognized experts on the hydrology and ecology of the Bay Delta was an efficient way to hear current knowledge on estuarine habitat, tools for modeling and assessing conditions, and how biological indicators and ecological processes respond to movement of the low salinity zone.  More specifically, the purpose of the workshop was to: Increase our collective understanding about the attributes of estuarine habitat, and the tools we have for protecting it Characterize the response of biological indicators and ecological processes to changing locations of the low salinity zone (LSZ) Generate scientific information that EPA and others can translate into recommendations that support the State’s Comprehensive Review of the 2006 Water Quality Control Plan (WQCP) for the Bay Delta Estuary The following sections describe planning for the workshop and the workshop process itself. The workshop summary condenses the input from participants during the small workgroup sessions and the final plenary session. It captures the breadth of opinions, judgments, and viewpoints expressed without attempting to fact check statements, or reconcile / synthesize disagreements or contradictions. Finally, the facilitator’s report provides my personal impressions of the workshop and the degree to which it achieved its stated purposes.