Use of the SmeltCam as an Efficient Fish-Sampling Alternative Within the San Francisco Estuary

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

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus). Although believed to be a reliable alternative to closed cod-end trawling surveys, no formal test of sampling efficiency has been implemented using the SmeltCam. We used a paired deployment of the SmeltCam and a conventional closed cod-end trawl within the Napa River and San Pablo Bay, a Bayesian binomial N-mixture model, and data simulations to determine the sampling efficiency of both deployed gear types to capture a Delta Smelt surrogate (Northern Anchovy, Engraulis mordax) and to test potential bias in our modeling framework. We found that retention efficiency—a component of detection efficiency that estimates the probability a fish is retained by the gear, conditional on gear contact—was slightly higher using the SmeltCam (mean = 0.58) than the conventional trawl (mean = 0.47, Probability SmeltCam retention efficiency > trawl retention efficiency = 94%). We also found turbidity did not affect the SmeltCam’s retention efficiency, although total fish density during an individual tow improved the trawl’s retention efficiency. Simulations also showed the binomial model was accurate when model assumptions were met. Collectively, our results suggest the SmeltCam to be a reliable alternative to sampling with conventional trawling gear, but future tests are needed to confirm whether the SmeltCam is as reliable when applied to taxa other than Northern Anchovy over a greater range of conditions.

User Manual for the California Central Valley Groundwater-Surface Water Simulation Model

California Department of Water Resources (DWR) | June 13th, 2013

This report describes the input and output files for the California Central Valley Groundwater-Surface Water Simulation Model (C2VSim). C2VSim is an integrated numeri

This report describes the input and output files for the California Central Valley Groundwater-Surface Water Simulation Model (C2VSim). C2VSim is an integrated numerical model simulating land surface processes and groundwater and surface water flows in the main alluvial aquifer system of California’s Central Valley (figure 1). C2VSim was developed using the Integrated Water Flow Model (IWFM) application, which couples a three-dimensional finite element groundwater simulation process with one-dimensional land surface, stream flow, lake, unsaturated zone and smallstream watershed simulation processes. The C2VSim version described in this report runs under IWFM version 3.02 and utilizes a coarse grid, and is thus referred to as version 3.02-CG. In addition, the input files for the C2VSim model are regularly updated to correct errors, incorporate improved input data or extend the simulation time period. These updates are referred to as revisions; this report describes the data in revision R374, released in June 2013. The C2VSim model inputs include monthly historical precipitation, stream inflows, surface water diversions, land use and crop acreages for the simulation period, October 1921 through September 2009. C2VSim dynamically calculates crop water demands, allocates contributions from precipitation, soil moisture and surface water diversions, and calculates the groundwater pumpage required to meet the remaining demand. The coarse grid version of the C2VSim model incorporates a finite element grid with 1392 elements, grouped into 21 water budget subregions (figure 1), which are further grouped by drainage basin into five hydrologic regions. The model subregions are based on Depletion Study Areas (DSAs), originally created by the DWR Division of Planning for estimating regional water supplies and demands. Hydrologic parameters (including hydraulic conductivities, storage parameters and recession coefficients) were calibrated to match observed values including groundwater heads, groundwater head differences between well pairs, surface water flows, and stream-groundwater flows for the period between September 1975 and October 2003. The model simulates the historical response of the Central Valley’s groundwater flow system to historical stresses, and can also be used to simulate the response to projected future stresses. Agricultural groundwater pumping is not monitored in the Central Valley, and the C2VSim model provides pumpage estimates that are considered robust because they are constrained spatially and temporally by the estimated demand and surface water supplies. The calibrated model is also being used as the basis for the groundwater flow component of CalSim 3, a water resources planning model for simulating operation of the California State Water Project (SWP) and Federal Central Valley Project (CVP).

Using Conceptual Models and Decision-Support Tools to Guide Ecosystem Restoration Planning and Adaptive Management: An Example from the Sacramento–San Joaquin Delta, California

University of California, Davis (UC Davis) | October 1st, 2012

The Sacramento–San Joaquin Delta (the Delta) is located on the western edge of California’s Central Valley and is of critical ecological and economic importance. H

The Sacramento–San Joaquin Delta (the Delta) is located on the western edge of California’s Central Valley and is of critical ecological and economic importance. However, ecosystem alterations for human uses changed many of the Delta’s natural processes, and it is now considered in need of restoration. An approach was developed to evaluate and rank restoration actions in the Delta under the Ecosystem Restoration Program’s Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The DRERIP approach provides an explicit framework for evaluating restoration actions, using linked conceptual models, an action evaluation procedure, and a decision-support tool. Conceptual models allow scientists and managers to synthesize scientific information and make qualitative predictions about ecosystem function and restoration outcomes to guide and focus restoration efforts. The action evaluation procedure is a structured assessment of restoration actions. The procedure clearly describes actions to be evaluated, assesses the magnitude (importance and scale) and certainty of anticipated ecological outcomes, estimates degrees of worth (achieving intended outcomes) and risk (causing adverse consequences), evaluates the reversibility of the action, and identifies opportunities for learning. The values for worthiness, risk, reversibility, and learning opportunity are used in the decision- support tool to determine the fate of a proposed action. The decision-support tool is a structured decision tree that determines the disposition of an action: whether a restoration project should be discarded, revised with a different approach and re-evaluated, or implemented; and, if implemented, at what scale (targeted research, pilot project, or full implementation). The DRERIP approach provides managers with a valuable tool for restoration planning, and a foundation for integration with quantitative methods for a comprehensive ecosystem restoration plan.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt

Nature Portfolio (Springer Nature) | December 1st, 2022

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in oto

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Vulnerability Assessments in Support of the Climate Ready Estuaries Program: A Novel Approach Using Expert Judgment, Volume I

U.S. Environmental Protection Agency (EPA) | January 1st, 2012

The San Francisco Bay estuary is highly vulnerable to climate - related changes including increased water temperatures, changes in precipitation and winds, and sea leve

The San Francisco Bay estuary is highly vulnerable to climate - related changes including increased water temperatures, changes in precipitation and winds, and sea level rise. Impacts such as increased inundation of coastal wetlands, changes in water availability and quality, and altered patterns of sedimentation and erosion are increasingly interacting with other human stressors such as extractive water uses and land use changes. Thus it is essential that estuary managers become ‘climate-ready’ by: assessing the vulnerability of natural resources to climate change; considering strategic choices among adaptation strategies in the near term; and engaging in longer term planning based on a range of plausible scenarios of future change. In an era of shrinking budgets coupled with increasingly complex decision-making needs—often taking place in a context of uncertainty and incomplete information— managing natural resources in the face of climate change will be challenging. There is a need for assessment methods that take advantage of existing scientific expertise to help identify robust adaptation strategies, weigh difficult trade-offs, and justify strong action, all in a timely and efficient manner. The purpose of this project was to carry out a pilot vulnerability assessment for the San Francisco Estuary Partnership’s (SFEP) natural resources using expert judgment, the results of which could be linked to adaptation planning. To this aim, EPA’s Office of Research and Development collaborated with SFEP and the San Francisco Bay Conservation and Development Commission on a novel expert elicitation exercise for ‘rapid’ vulnerability assessment. A trial exercise was carried out during a two-day workshop in which two groups of seven experts each focused on two key ecosystem processes: sediment retention in salt marshes and community interactions of shorebirds with their predators and prey (see Figure ES - 1). The exercise, which was based on formal expert elicitation techniques but tailored specifically for qualitative analysis of ecosystem processes, was designed to glean expert information on the sensitivities of ecosystem process components under future climate scenarios . This was followed by group discussions of the implications of the results for management in light of climate change, as well as feedback on the exercise itself.  

Water Column Selenium Concentrations in the San Francisco Bay-Delta: Recent Data and Recommendations for Future Monitoring

San Francisco Estuary Institute (SFEI) | August 1st, 2017

The San Francisco Bay Regional Water Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB) in 2015.1 T

The San Francisco Bay Regional Water Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB) in 2015.1 The TMDL is based on attainment of water column and fish tissue target concentrations protective of human health, aquatic life, and wildlife, and was approved by the US Environmental Protection Agency in August, 2016. Analyses in support of the TMDL synthesized the results of different monitoring efforts to characterize selenium concentrations in water and biota in the Estuary. For water quality evaluation in the TMDL, the sources of observational data included studies of selenium speciation across the estuarine salinity gradient, performed in 1999-2000 and again in 2010 and 2012 (Cutter and Cutter 2004, Doblin et al. 2006, Tetra Tech, 2012), as well as samples collected by the San Francisco Bay Regional Monitoring Program (RMP). Changes in wastewater treatment from the five major refineries in NSFB were implemented in the late 1990s, leading to significant reductions in selenium loads. Data at Estuary center-line locations showed small changes for dissolved selenium in the mid-salinity range and no trends in particulate selenium (Baginska, 2015). As part of the TMDL, water quality modeling analyses were performed to characterize NSFB selenium concentrations under a range of hydrologic conditions and changing point-source loads (Baginska, 2015). Water column selenium concentration data in the NSFB and Delta continue to be collected at selected locations, although these data have not been systematically evaluated following the analyses presented in the TMDL reports. In the near term, possible changes that may cause selenium concentrations to change in the NSFB and Delta include concentration changes in the inflow from the San Joaquin River basin, changes in refinery inputs, changes in stormwater and tributary loads from the Bay margin, and changes in overall Central Valley hydrological conditions, such as the extreme wet and dry periods that occurred between 2012 and 2017. Other drivers, such as nutrient concentrations and algal levels, may also play a role, especially on the concentrations of selenium on particulates.

Water Facilities Including a Peripheral Canal [Proposition 9]

Department of Justice (DOJ) | June 9th, 1982

Water for a Growing Bay Area: How the region can grow without increasing water demand

Pacific Institute | October 21st, 2021

The San Francisco Bay Area is at a crossroads. The region, blessed with a beautiful natural setting, multiple shipping ports and world-class universities, is a driver of

The San Francisco Bay Area is at a crossroads. The region, blessed with a beautiful natural setting, multiple shipping ports and world-class universities, is a driver of global economic growth. But the region’s housing supply has not kept up with population growth. Many low-income households, disproportionately made up of people of color, have been forced into overcrowded and substandard housing or displaced from the urban center to new neighborhoods far from their jobs, friends and families. The most vulnerable have lost their homes entirely and are among the region’s 35,000 unhoused people. Over the next half-century, the Bay Area’s need to add housing will only grow more intense. The region is projected to add 2 million new jobs by 2070, which would attract as many as 6.8 million people, and needs to build at least 2.2 million new housing units just to prevent housing affordability from worsening. This represents 83% more people, 74% more housing units and 38% more jobs over the next 50 years.

Water management in mediterranean river basins: a comparison of management frameworks, physical impacts, and ecological responses

Hydrobiologia (Springer) | September 11th, 2012

Rivers in mediterranean climates have been extensively modified by water management infrastructure and practices, yet patterns of development and consequent effec

Rivers in mediterranean climates have been extensively modified by water management infrastructure and practices, yet patterns of development and consequent effects on freshwater ecosystems have not been compared across multiple regions. To evaluate the influence of water management on mediterranean-climate rivers, we compare the historic progression of management policies, institutions, and ecosystem impacts in the Sacramento River (California, USA), Ebro River (Spain), and Biobío River (Chile) basins. There are broad similarities in patterns of ecosystem alterations related to the extensive development of dams and water management infrastructure in the three study basins. Flow regimes have been altered by the reduction of winter peak flows and increased summer baseflows. There are also common patterns of disturbance from sediment transport alteration, water quality degradation, and declines in freshwater biodiversity. Current approaches are inadequate for addressing the formidable water management challenges in California, Spain, and Chile, yet the dramatic evolution of water policies and institutions over the past 150 years suggests that further adaptation is possible. Advances toward integrated and sustainable water management models are likely to occur through incremental change, driven by growing awareness of climate change effects and public demands for water-use efficiency and improved environmental quality.  

Water Quality Challenges in the San Francisco Bay/ Sacramento-San Joaquin Delta Estuary: EPA’s Action Plan

U.S. Environmental Protection Agency (EPA) | August 22nd, 2012

The U.S. Environmental Protection Agency (EPA) developed this Action Plan after assessing the effectiveness of current regulatory mechanisms designed to protect water qua

The U.S. Environmental Protection Agency (EPA) developed this Action Plan after assessing the effectiveness of current regulatory mechanisms designed to protect water quality in the San Francisco Bay Sacramento-San Joaquin Delta Estuary (Bay Delta Estuary) and its tributaries. EPA’s assessment concludes that Clean Water Act (CWA) programs currently are not adequately protecting aquatic resources of the Bay Delta Estuary. In this document, EPA recommends actions to restore water quality for aquatic species protection using existing EPA authorities and resources, as well as actions EPA believes are important and appropriate for the State Water Resources Control Board (State Water Board). EPA is one of more than 25 state and federal governmental agencies with responsibilities in the Bay Delta Estuary. EPA’s major statutory mission in the Estuary is to implement the CWA. EPA has delegated many CWA program authorities to the State Water Board while providing financial support,1 technical assistance, and oversight (including, in some cases, review and approval of State actions). Much of EPA's work in this Action Plan (as well as elsewhere in California) is done in support of and in partnership with the State. For example, water quality standards, which define water quality goals for our waterbodies, are typically developed and adopted by the State with EPA assistance, review, and ultimately, approval or disapproval. In the Bay Delta Estuary, EPA focuses on assuring that the many designated uses of the Estuary’s aquatic resources are protected. EPA emphasizes the CWA goals of maintaining and improving water quality – the chemical, physical, and biological integrity of the water – to ensure the Bay Delta Estuary can function as a vibrant, healthy estuary. About 90 species of fish are found in the Delta. The Delta’s channels serve as a migratory route and nursery area for Chinook salmon, striped bass, white and green sturgeon, American shad, and steelhead trout. These anadromous fish spend most of their adult lives either in the lower bays of the Estuary or in the ocean. Resident fish in the Estuary include delta smelt, longfin smelt, Sacramento splittail, catfish, largemouth bass, black bass, crappie, and bluegill. All Bay Delta Estuary waters are impaired by one or more contaminants. In addition, the reduction in the quantity and quality of estuarine habitat limits the Estuary’s ability to support aquatic species. EPA’s Action Plan describes a suite of activities to: 1. Strengthen water quality standards to protect estuarine habitat 2. Advance regional water quality monitoring and assessment 3. Accelerate water quality restoration through Total Maximum Daily Loads 4. Strengthen selenium water quality criteria 5. Prevent pesticide pollution 6. Restore aquatic habitats while managing methylmercury 7. Support the Bay Delta Conservation Plan Collectively, these activities will contribute to the restoration of the Bay Delta Estuary. Even if they are all successfully implemented, however, they are not sufficient to resolve the complex problems that have stressed the ecosystem to the point of collapse. Any solution to the ecological problems of the Bay Delta Estuary must be multi-faceted, including providing sufficient flows, physical habitat which is sufficiently large, connected, diverse, and self-sustaining, as well as a reduction of many types of stressors, such as contaminants, invasive species, and predation.