Dimension reduction approach for understanding resource-flow resilience to climate change

Nature Portfolio (Springer Nature) | June 15th, 2024

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.

Dissolved Pesticide Concentrations Entering the Sacramento–San Joaquin Delta from the Sacramento and San Joaquin Rivers, California, 2012–13

U.S. Geological Survey (USGS) | August 20th, 2014

Surface-water samples were collected from the Sacramento and San Joaquin Rivers where they enter the Sacramento–San Joaquin Delta, and analyzed by the U.S. Geological S

Surface-water samples were collected from the Sacramento and San Joaquin Rivers where they enter the Sacramento–San Joaquin Delta, and analyzed by the U.S. Geological Survey for a suite of 99 current-use pesticides and pesticide degradates. Samples were collected twice per month from May 2012 through July 2013 and from May 2012 through April 2013 at the Sacramento River at Freeport, and the San Joaquin River near Vernalis, respectively. Samples were analyzed by two separate laboratory methods by using gas chromatography with mass spectrometry or liquid chromatography with tandem mass spectrometry. Method detection limits ranged from 0.9 to 10.5 nanograms per liter (ng/L). A total of 37 pesticides and degradates were detected in water samples collected during the study (18 herbicides, 11 fungicides, 7 insecticides, and 1 synergist). The most frequently detected pesticides overall were the herbicide hexazinone (detected in 100 percent of the samples); 3,4-dichloroaniline (97 percent), which is a degradate of the herbicides diuron and propanil; the fungicide azoxystrobin (83 percent); and the herbicides diuron (72 percent), simazine (66 percent), and metolachlor (64 percent). Insecticides were rarely detected during the study. Pesticide concentrations varied from below the method detection limits to 984 ng/L (hexazinone).

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 Monitoring Special Study Plan

California State Water Resources Control Board (SWRCB) | August 15th, 2022

Delta Estuary (Bay–Delta Plan), as amended through 2006, the State Water Resources Control Board (State Water Board) set salinity objectives for the interior southern D

Delta Estuary (Bay–Delta Plan), as amended through 2006, the State Water Resources Control Board (State Water Board) set salinity objectives for the interior southern Delta. In Water Right Decision 1641 (D-1641), as part of the implementation of the 1995 Bay–Delta Plan, the California Department of Water Resources (DWR) and U.S. Bureau of Reclamation (Reclamation) were assigned partial responsibility for meeting these objectives, including maintaining Specific Conductance (EC) levels at three monitoring stations (Interagency Stations No. C-6, C-8, and P-12) in the interior southern Delta waterways (Figure 3-1)1. In 2018, the State Water Board adopted amendments to the Bay–Delta Plan. Per the 2018 Bay-Delta Plan amendments, DWR and Reclamation are working to develop a Monitoring Special Study (MSS). This document serves as the study plan for the MSS and identifies three goals, consistent with section B(1)(iv) of the 2018 Bay–Delta Plan. Since early 2021, using best-science practices, DWR and Reclamation have been soliciting input from participating agencies and working with State Water Board staff to design technical studies to accomplish the following goals. 1) Characterize the spatial and temporal distribution and associated dynamics of water level, flow, and salinity conditions in the southern Delta waterways. 2) Identify the extent of low- or null-flow conditions and any associated concentration of local salt discharges. 3) Inform the development of a Long-Term Monitoring and Reporting Plan that will: a. Assess attainment of the salinity objective in the interior southern Delta; and b. Include long-term monitoring and reporting protocols, including specific compliance monitoring locations in, or monitoring protocols for, the three river segments that comprise the interior southern Delta salinity compliance locations.

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

DRERIP Ecosystem Conceptual Model: Chemical stressors

California Department of Fish and Wildlife (CDFW) | February 5th, 2008

The Sacramento-San Joaquin Delta ecosystem comprises many different habitat types, and is home to a large number of species. Thousands of chemical contaminants have been

The Sacramento-San Joaquin Delta ecosystem comprises many different habitat types, and is home to a large number of species. Thousands of chemical contaminants have been or are being introduced into the Delta. The conceptual model presented here is therefore general in nature, and is intended to provide a framework for more refined models for individual species, habitats and, in particular, contaminants of interest, for example selenium, mercury and pyrethroids. The model consists of three major submodels (Figure 1). Submodel 1: Exposure assessment which includes fate and transport of contaminants and the co-occurrence of chemicals with Delta organisms; the intermediate outcome of this submodel is “Exposure Concentration”. Submodel 2: Bioavailability of contaminants to Delta organisms; the intermediate outcome of this submodel is “Bioavailable Concentration” or “Dose”.  Submodel 3: Toxic effects assessment with the final model outcome “Population Level Effects”. In the following narrative, we provide a description for each submodel, its parameters, and linkages to other models. We discuss the model’s limitations and provide recommendations for its application in management.

DRERIP Ecosystem Conceptual Model: Chinook Salmon & Steelhead

California Department of Fish and Wildlife (CDFW) | September 4th, 2012

This report constitutes the conceptual model for Chinook and steelhead for the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The report describes

This report constitutes the conceptual model for Chinook and steelhead for the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The report describes conceptual models, not numerical models, but several important considerations apply to both kinds, especially when they are used for management of living natural resources. First, the proper purpose of models is to help people think, not to think for them. Ignoring this can be disastrous, as exemplified by the current economic crisis. The world of credit default swaps was built on highly sophisticated models that persuaded many intelligent people that the associated risk was negligible, but they failed to recognize that a market based on houses that people could not pay for from their earnings is unsustainable. In short, the most important output of a good conceptual or numerical model is clear thinking. To help people think, the model must be focused on selected features of the world that are thought to be important for the purpose at hand: in this case, management of the Delta. A model that tries to include everything will be too complex to be useful for this purpose. Second, to be useful for management of natural living resources, numerical models must be unrealistic, because our knowledge of such resources is incomplete, and is based on data that includes measurement errors. According to Ludwig‘s paradox, "Effective management models cannot be realistic" (Ludwig 1994:516), because two kinds of uncertainty must be balanced (Figure I-1; see Ch. 14 in Williams (2006) for elaboration of this point). In our view, something similar applies to conceptual models of natural systems: to be useful, they must be simple. A schematic of the wiring in some electronic device is a conceptual model that may be useful as well as complex, but trying to develop a similar schematic of an ecosystem or part of an ecosystem is not useful, because our knowledge of such a system is much less complete than our knowledge of engineered devices, and we have only estimates of the relevant parameters. Finally, reality is too complex to capture with a single model. Eric Lander, a noted geneticist who co-chairs President Obama‘s Council of Advisors on Science and Technology, recently remarked that "You can never capture something like an economy, a genome or an ecosystem with one model or one taxonomy – it all depends on the questions you want to ask." (NY Times, 11/11/08). Models are tools that we use to try to think, and multi-purpose tools generally do nothing well. Therefore, although the complete life cycle of Chinook and steelhead is described here, the parts or aspects of the cycle that we think may be affected by management of the Delta are emphasized, and we try to keep it as simple as possible. More detail on most of the topics described here can be found in Quinn (2005), or in Williams (2006), from which this document draws very heavily.