Delta-Estuary California's Inland Coast A Public Trust Report

California State Lands Commission (SLC) | May 1st, 1991

Demonstration of a Watershed Approach to Wetland Restoration Planning for Load Reductions: A Pilot Demonstration Project Using GreenPlan-IT in the Santa Rosa Plain, Sonoma County, California

San Francisco Estuary Institute (SFEI) | December 30th, 2017

This summary memorandum presents technical recommendations to the 401 Certification and Waste Discharge Program (401 Program) of the State Water Resources Control Board (

This summary memorandum presents technical recommendations to the 401 Certification and Waste Discharge Program (401 Program) of the State Water Resources Control Board (State Board) for a coherent, scientifically sound, repeatable, watershed approach to wetland restoration site evaluation, compliance monitoring and assessment, and Tracking. The recommendations are drawn from the previous four memoranda produced for the Pilot Demonstration Project (Project) that address the following subjects: project work plan and information flow diagram; scientific literature review; landscape scenario planning (to map and prioritize restoration opportunities); and a framework for a watershed-approach to evaluate and report the capacity of a wetland restoration site to protect wetland beneficial uses. This Project focused on a sub-watershed of the Santa Rosa Plain, in Sonoma County, California. The area was chosen for the Project for three reasons: (1) it is integral to an existing nutrient TMDL and therefore is supported relatively well with hydrological and nutrient data; (2) the historical and existing wetlands and streams of the area were mapped recently in sufficient detail to inform landscape planning; and (3) implementation of the TMDL will involve wetland restoration to reduce downstream nutrient loads, and therefore the Project may help implement the TMDL. The primary overall purpose of this Project was to explore how numerical simulation and statistical modeling could be combined with existing wetland assessment and reporting tools to create a coherent, watershed-based approach to wetland beneficial use protection. Any relevance to the existing nutrient TMDL for the demonstration area is an intentional, but secondary benefit of this Project. Contents: Wetland Beneficial Use Protection: Pilot Demonstration Project A Synthesis of Literature on Wetland Assimilation Capacities, Models, and Pollutant Loads Simulating Wetland Assimilation Capacity in the Lower Santa Rosa Creek Watershed Pilot Demonstration Area Using the HSPF Model Demonstration of a Watershed Approach To Wetland Restoration Planning Using GreenPlan-IT

Department of Fish and Game Rationale for Effects of Exports

California Department of Fish and Wildlife (CDFW) | November 2nd, 2011

This document describes the California Department of Fish and Game (DFG) methodology to quantify the surface area in the Sacramento – San Joaquin delta estuary (Delta)

This document describes the California Department of Fish and Game (DFG) methodology to quantify the surface area in the Sacramento – San Joaquin delta estuary (Delta) that is impacted by the operations of the State Water Project (SWP) and Central Valley Project (CVP) pumping facilities. In order to estimate the mitigation required to offset direct and indirect losses of Fish Species due to impacts to surface acres of aquatic habitat in the Delta accounted to the SWP Delta Pumping Facilities operations, DFG used an analysis based on conclusions and information contained in a manuscript that utilizes the Delta Simulation Model-2 Particle Tracking Model (DSM2PTM) (Kimmerer and Nobriga, 2008). This methodology provides the general loss of “particles” to the Delta which is a surrogate for loss of productivity and fish life stages vulnerable to these effects.

Depletion and Capture: Revisiting “The Source of Water Derived from Wells”

National Groundwater Association (NGWA) | May 28th, 2014

A natural consequence of groundwater withdrawals is the removal of water from subsurface storage, but the overall rates and magnitude of groundwater depletion and capture

A natural consequence of groundwater withdrawals is the removal of water from subsurface storage, but the overall rates and magnitude of groundwater depletion and capture relative to groundwater withdrawals (extraction or pumpage) have not previously been well characterized. This study assesses the partitioning of long‐term cumulative withdrawal volumes into fractions derived from storage depletion and capture, where capture includes both increases in recharge and decreases in discharge. Numerical simulation of a hypothetical groundwater basin is used to further illustrate some of Theis' (1940) principles, particularly when capture is constrained by insufficient available water. Most prior studies of depletion and capture have assumed that capture is unconstrained through boundary conditions that yield linear responses. Examination of real systems indicates that capture and depletion fractions are highly variable in time and space. For a large sample of long‐developed groundwater systems, the depletion fraction averages about 0.15 and the capture fraction averages about 0.85 based on cumulative volumes. Higher depletion fractions tend to occur in more arid regions, but the variation is high and the correlation coefficient between average annual precipitation and depletion fraction for individual systems is only 0.40. Because 85% of long‐term pumpage is derived from capture in these real systems, capture must be recognized as a critical factor in assessing water budgets, groundwater storage depletion, and sustainability of groundwater development. Most capture translates into streamflow depletion, so it can detrimentally impact ecosystems.

Desalination Plant Entrainment Impacts and Mitigation

California State Water Resources Control Board (SWRCB) | October 9th, 2013

Raw seawater is used for a variety of purposes, including as source water for desalination plants and to cool coastal power plants. Raw seawater is, however, not just col

Raw seawater is used for a variety of purposes, including as source water for desalination plants and to cool coastal power plants. Raw seawater is, however, not just cold and salty but an ecosystem that contains diverse and abundant organisms including the young stages of numerous invertebrates and fishes. Whether impinged (large individuals stuck on screens prior to entering the plant or killed during other plant processes such as heat treatment) or entrained (small individuals carried into the plant with the water) the organisms are killed, essentially eliminating the living production in the water used (review in York and Foster 2005). Considerable research has have been done in California to better estimate losses to this ecosystem by coastal power plant intakes (York and Foster 2005, Steinbeck et al. 2007), and to determine how these losses can be mitigated (Strange et al. 2004). The information from this research has contributed to State of California policy regulating water used by power plants.

Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem

California State Water Resources Control Board (SWRCB) | August 4th, 2010

Water Code section 85086 (See Appendix B), contained in the Delta Reform Act, was enacted as part of the comprehensive package of water legislation adopted in November 20

Water Code section 85086 (See Appendix B), contained in the Delta Reform Act, was enacted as part of the comprehensive package of water legislation adopted in November 2009. Water Code section 85086 requires the State Water Resources Control Board (State Water Board) to use the best available scientific information gathered as part of a public process conducted as an informational proceeding to develop new flow criteria for the Delta ecosystem to protect public trust resources. The purpose of the flow criteria is to inform planning decisions for the Delta Plan and the BDCP. The Legislature intended to establish an accelerated process to determine the instream flow needs of the Delta in order to facilitate the planning decisions required to meet the objectives of the Delta Plan. Accordingly, Water Code section 85086 requires the State Water Board to develop the flow criteria within nine months of enactment of the statute and to submit its flow criteria determinations to the Council within 30 days of their development. This report, required by Water Code section 85086(c) (2009 Delta Reform Act) in 2010, suggests the flows that would be needed in the Delta ecosystem if fishery protection was the sole purpose for which its waters were put to beneficial use. In keeping with the narrow focus of the legislation, this report only presents a technical assessment of flow and operational requirements to provide fishery protection under existing conditions.  

Development of Recommended Flow Targets to Support Biological Integrity Based on Regional Flow-ecology Relationships for Benthic Macroinvertebrates in Southern California Streams

Southern California Coastal Water Research Project | March 23rd, 2017

Changes to instream flow are known to be one of the major factors that affect the health of biological communities. Regulatory, monitoring, and management programs are in

Changes to instream flow are known to be one of the major factors that affect the health of biological communities. Regulatory, monitoring, and management programs are increasingly using biological community composition, particularly benthic invertebrates, as one measure of instream conditions, stormwater project performance, or regulatory compliance with NPDES or other requirements and regulations. Understanding the relationship between changes in flow and changes in benthic invertebrate communities is, therefore, critical to informing decisions about ecosystem vulnerability, causes of stream and watershed degradation, and priorities for future watershed management. There are many approaches to developing flow-ecology relationships that relate hydrologic change to responses in instream biological communities that can be used to establish management targets. The Ecological Limits of Hydrologic Alteration (ELOHA) framework (Poff et al. 2010) provides a way to assess the effect of flow alteration on the condition of biological communities (vs. individual taxa) on a regional basis. Consequently, it is a useful approach for setting targets across a wide range of geographies and stream types where comprehensive detailed site-specific investigations are not practical. The framework includes elements of stream classification, estimation of flow alteration and development of flow ecology relationships based on the response of biological communities to changes in flow.

DISB Review of Bay Delta Conservation Plan/California WaterFix Partially Recirculated Draft EIR/EIS

Delta Stewardship Council (Delta Council) | October 1st, 2015

We have reviewed the partially Recirculated Draft Environmental Impact Report/ Supplemental Draft Environmental Impact Statement for the Bay Delta Conservation Plan/Calif

We have reviewed the partially Recirculated Draft Environmental Impact Report/ Supplemental Draft Environmental Impact Statement for the Bay Delta Conservation Plan/California WaterFix (herein, "the Current Draft"). We focused on how fully and effectively it considers and communicates the scientific foundations for assessing the environmental impacts of water conveyance alternatives. The review is attached and is summarized below. The Current Draft contains a wealth of information but lacks completeness and clarity in applying science to far-reaching policy decisions. It defers essential material to the Final EIR/EIS and retains a number of deficiencies from the Bay Delta Conservation Plan Draft EIR/EIS. The missing content includes: 1. Details about the adaptive-management process, collaborative science, monitoring, and the resources that these efforts will require; 2. Due regard for several aspects of habitat restoration: landscape scale, timing, long-term monitoring, and the strategy of avoiding damage to existing wetlands; 3. Analyses of how levee failures would affect water operations and how the implemented project would affect the economics of levee maintenance; 4. Sufficient attention to linkages among species, landscapes, and management actions; effects of climate change on water resources; effects of the proposed project on San Joaquin Valley agriculture; and uncertainties and their consequences; 5. Informative summaries, in words, tables, and graphs, that compare the proposed alternatives and their principal environmental and economic impacts. The effects of California WaterFix extend beyond water conveyance to habitat restoration and levee maintenance. These interdependent issues of statewide importance warrant an environmental impact assessment that is more complete, comprehensive, and comprehensible than the Current Draft.

Disentangling Stationary and Dynamic Estuarine Fish Habitat to Inform Conservation: Species-Specific Responses to Physical Habitat and Water Quality in San Francisco Estuary

American Fisheries Society (AFS) | October 12th, 2021

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, wh

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, which provide important habitat for fishes and other aquatic organisms. Effective conservation of species inhabiting estuaries requires knowledge of the habitat features that drive their abundance and distribution. We sought to elucidate how stationary (i.e., wetlands, shoals, and channels) and dynamic (i.e., salinity, temperature, turbidity, and chlorophyll concentration) habitat features interact to drive distributions of individual fish species. The Pacific coast of the conterminous United States has over 400 estuaries of various types. The largest (historical surface area) is San Francisco Estuary, California. We conducted extensive field observations of fishes in the central San Francisco Estuary among stationary habitat types (i.e., wetland, shoal, and channel) over a 19-month period encompassing substantial variability in dynamic water quality conditions. Most of the species observed, especially native species of special management interest, were associated with tidal wetland habitat. Few species exhibited associations with water quality conditions driven by seasonal (temperature) or a combination of broad- and fine-scale ecosystem processes (salinity and turbidity). Our study provides (1) an empirical demonstration of how researchers can deal with the complex and dynamic expressions of habitat in estuarine systems to address urgent natural resource problems and (2) a clear demonstration of the urgent need for habitat restoration and its likely outcome in systems such as San Francisco Estuary. Restoration of suitable tidal wetland habitat on the West Coast of the United States is likely to be an effective conservation tool to support estuarine fishes given that over 90% of historical tidal wetland habitat in San Francisco Estuary and 85% of vegetated wetland habitat along the Pacific coast of the United States has been lost due to human modification.

Dispersion and Stratification Dynamics in the Upper Sacramento River Deep Water Ship Channel

University of California, Davis (UC Davis) | December 1st, 2021

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosyste

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosystems through their influence on primary production. The San Francisco Estuary (estuary) is a low-productivity ecosystem, which is in part responsible for constraining higher trophic levels, including fishes. Many research and habitat-restoration efforts trying to increase primary production have been conducted, including, as described here, a whole-ecosystem nutrient addition experiment where calcium nitrate was applied in the Sacramento River Deep Water Ship Channel (DWSC) to see if phytoplankton production could be increased and exported out of the DWSC. As an integral part of this experiment, we investigated the physical mechanisms that control mixing, and how these mechanisms affect the strength and duration of thermal stratification, which we revealed as critical for controlling phytoplankton dynamics in the relatively turbid upper DWSC. Analysis of a suite of mixing mechanisms and time-scales show that both tidal currents and wind control mixing rates and stratification dynamics in the DWSC. Longitudinal and vertical dispersion increased during periods of high wind, during which wind speed influenced dispersion more than tidal currents. Thermal stratification developed most days, which slowed vertical mixing but was rapidly broken down by wind-induced mixing. Stratification rarely persisted for longer than 24 hours, limiting phytoplankton production in the study area. The interaction between physical mechanisms that control mixing rates, mediate stratification dynamics, and ultimately limit primary production in the DWSC may be useful in informing habitat restoration elsewhere in the Delta and in other turbid aquatic environments.