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.

Dissolved Oxygen in South San Francisco Bay: Variability, Important Processes, and Implications for Understanding Fish Habitat

San Francisco Estuary Institute (SFEI) | October 30th, 2018

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Inst

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Institute (SFEI) launched a study to investigate the potential effects of low-DO on habitat quality in Lower South Bay (LSB) to inform decisions about nutrient regulation. The goal of the study was to understand where and when regions of LSB provide adequate DO to support resident fish species. The study approach involved convening a team of experts to advise on methods, analyzing high frequency DO measurements from seven mooring stations in LSB, and partnering with researchers from UC Davis to interpret several years of monthly fish abundance data in LSB relative to DO and other factors.

Documentation of a Groundwater Flow Model (SJRRPGW) for the San Joaquin River Restoration Program Study Area, California

U.S. Geological Survey (USGS) | September 23rd, 2014

To better understand the potential effects of restoration flows on existing drainage problems, anticipated as a result of the San Joaquin River Restoration Program (SJRRP

To better understand the potential effects of restoration flows on existing drainage problems, anticipated as a result of the San Joaquin River Restoration Program (SJRRP), the U.S. Geological Survey (USGS), in cooperation with the U.S. Bureau of Reclamation (Reclamation), developed a groundwater flow model (SJRRPGW) of the SJRRP study area that is within 5 miles of the San Joaquin River and adjacent bypass system from Friant Dam to the Merced River. The primary goal of the SJRRP is to reestablish the natural ecology of the river to a degree that restores salmon and other fish populations. Increased flows in the river, particularly during the spring salmon run, are a key component of the restoration effort. A potential consequence of these increased river flows is the exacerbation of existing irrigation drainage problems along a section of the river between Mendota and the confluence with the Merced River. Historically, this reach typically was underlain by a water table within 10 feet of the land surface, thus requiring careful irrigation management and (or) artificial drainage to maintain crop health. The SJRRPGW is designed to meet the short-term needs of the SJRRP; future versions of the model may incorporate potential enhancements, several of which are identified in this report. The SJRRPGW was constructed using the USGS groundwater flow model MODFLOW and was built on the framework of the USGS Central Valley Hydrologic Model (CVHM) within which the SJRRPGW model domain is embedded. The Farm Process (FMP2) was used to simulate the supply and demand components of irrigated agriculture. The Streamflow-Routing Package (SFR2) was used to simulate the streams and bypasses and their interaction with the aquifer system. The 1,300-square mile study area was subdivided into 0.25-mile by 0.25-mile cells. The sediment texture of the aquifer system, which was used to distribute hydraulic properties by model cell, was refined from that used in the CVHM to better represent the natural heterogeneity of aquifer-system materials within the model domain. In addition, the stream properties were updated from the CVHM to better simulate stream-aquifer interactions, and water-budget subregions were refined to better simulate agricultural water supply and demand. External boundary conditions were derived from the CVHM. The SJRRPGW was calibrated for April 1961 to September 2003 by using groundwater-level observations from 133 wells and streamflow observations from 19 streamgages. The model was calibrated using public-domain parameter estimation software (PEST) in a semi-automated manner. The simulated groundwater-level elevations and trends (including seasonal fluctuations) and surface-water flow magnitudes and trends reasonably matched observed data. The calibrated model is planned to be used to assess the potential effects of restoration flows on agricultural lands and the relative capabilities of proposed SJRRP actions to reduce these effects.

Downscaling global ocean climate models improves estimates of exposure regimes in coastal environments

Nature Portfolio (Springer Nature) | August 26th, 2020

Climate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these pred

Climate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these predictions are then often used to parameterize laboratory experiments designed to assess biological and ecological responses to future change. However, nearshore ecosystems are affected by a range of physical processes such as tides, local winds, and surface and internal waves, causing local variability in conditions that often exceeds global climate models. Predictions of future climatic conditions at local scales, the most relevant to ecological responses, are largely lacking. To fill this critical gap, we developed a 2D implementation of the Regional Ocean Modeling System (ROMS) to downscale global climate predictions across all Representative Concentration Pathway (RCP) scenarios to smaller spatial scales, in this case the scale of a temperate reef in the northeastern Pacific. To assess the potential biological impacts of local climate variability, we then used the results from different climate scenarios to estimate how climate change may affect the survival, growth, and fertilization of a representative marine benthic invertebrate, the red abalone Haliotis rufescens, to a highly varying multi-stressor environment. We found that high frequency variability in temperature, dissolved oxygen (DO), and pH increases as pCO2 increases in the atmosphere. Extreme temperature and pH conditions are generally not expected until RCP 4.5 or greater, while frequent exposure to low DO is already occurring. In the nearshore environment simulation, strong RCP scenarios can affect red abalone growth as well as reduce fertilization during extreme conditions when compared to global scale simulations.

Draft finding of no significant impact, 2-Gates Fish Protection Demonstration Project.

U.S. Bureau of Reclamation (USBR) | November 13th, 2009

The proposed Demonstration Project is a 5-year experiment to validate a new delta smelt behavioral model and study the effects of modifying flows in the Sacramento-San Jo

The proposed Demonstration Project is a 5-year experiment to validate a new delta smelt behavioral model and study the effects of modifying flows in the Sacramento-San Joaquin Delta (Delta) to protect delta smelt and other sensitive aquatic species from entrainment in Central Valley Project (CVP) and State Water Project (SWP) export pumps. Research suggests that the pre-spawning migration of adult delta smelt is tied to sediment/suspended particles in the water (turbidity). Temporary gates would be placed across Old River and Connection Slough in the central Delta and operated from December to March to keep turbid water away from the CVP and SWP export pumps, thus keeping adult delta smelt away from the pumps, and in March and June to prevent larvae and juvenile delta smelt from being entrained by the export pumps.

DRAFT Staff Report/Substitute Environmental Document in Support of Potential Updates to the Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary for the Sacramento River and its Tributaries, Delta Eastside Tributaries, and Delta

California State Water Resources Control Board (SWRCB) | September 28th, 2023