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

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.

DRERIP Ecosystem Conceptual Model: Delta Aquatic Foodweb

California Department of Fish and Wildlife (CDFW) | October 3rd, 2008

This model is a stylization of the actual food web dynamics of the Sacramento-San Joaquin Delta, which are highly dynamic. The region itself comprises a variety of habita

This model is a stylization of the actual food web dynamics of the Sacramento-San Joaquin Delta, which are highly dynamic. The region itself comprises a variety of habitats, determined by salinity regimes, residence time, hydrology, benthos and physical structure. These physical parameters, or drivers, determine species composition and trophic relationships. The Delta is a tidal system which is subject to varying water inflow. Because inflow and outflow vary as the result of anthropogenic alterations and water management needs, habitats are not static. Rather they are subject to hourly, daily, seasonal and inter-annual variation, and different organisms respond in different ways to these time scales, depending upon their own life histories. Thus salinity and temperature regimes may create different outcomes from food web interactions, based upon how species distributional and recruitment patterns overlap. In general, food web linkages are not static or linear. Organisms switch feeding strategies opportunistically, and these patterns of variability in feeding strategy tend to increase with trophic level. Many organisms, particularly plankton, undergo many generations in the course of a year, and selective forces may allow for rapid evolution which can alter habitat preferences or other life history characteristics. The Delta food web is further dynamic in that new species are regularly introduced into the Estuary, competing with, replacing, or preying upon other organisms. For example, the overbite clam, Corbula amurensis, was introduced in 1986, precipitating a cascade of changes that are still not wholly understood. Zebra and quagga mussels are expected to invade the Delta within the next few years, and will bring further changes. The topology of a food web model will be necessarily complex given these factors. Even without such variability, the potential linkages create a spider web of relationships that is difficult if not impossible to disentangle. In order to create a working model of the Delta food web that is useful for education, for hypothesis?generation, and for management decision?making, it is necessary to create limits to what linkages will be examined. In order to do this, this Delta food web model focuses on organisms that supply food for fish. This is particularly important given the recent concern for pelagic organism decline, which is described mostly for fishes, some of which are listed as endangered or threatened. A key assumption is that fish are integrators of ecosystem function. Also included in the model are invasive organisms that have a large impact on food web dynamics (such as C. amurensis), as are organisms that are particularly abundant (such as the copepod Limnoithona tetraspina), whether or not they are used directly by fish.

DRERIP Ecosystem Conceptual Model: Delta smelt

California Department of Fish and Wildlife (CDFW) | October 22nd, 2010

This Conceptual Model is part of a suite of conceptual models which collectively articulate the current scientific understanding of important aspects of the Sacramento-Sa

This Conceptual Model is part of a suite of conceptual models which collectively articulate the current scientific understanding of important aspects of the Sacramento-San Joaquin River Delta ecosystem. The conceptual models are designed to aid in the identification and evaluation of ecosystem restoration actions in the Delta. These models are designed to structure scientific information such that it can be used to inform sound public policy. The Delta Conceptual Models include both ecosystem element models (including process, habitat, and stressor models) and species life history models. The models were prepared by teams of experts using common guidance documents developed to promote consistency in the format and terminology of the models http://www.delta.dfg.ca.gov/erpdeltaplan/science_process.asp . The Delta Conceptual Models are qualitative models which describe current understanding of how the system works. They are designed and intended to be used by experts to identify and evaluate potential restoration actions. They are not quantitative, numeric computer models that can be “run” to determine the effects of actions. Rather they are designed to facilitate informed discussions regarding expected outcomes resulting from restoration actions and the scientific basis for those expectations. The structure of many of the Delta Conceptual Models can serve as the basis for future development of quantitative models.