Sacramento River

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.

Using Landsat and MODIS satellite collections to examine extent, timing, and potential impacts of surface water inundation in California croplands

Remote Sensing Applications: Society and Environment (RSASE) | October 1st, 2022

The state of California, United States of America produces many crop products that are both utilized domestically and exported throughout the world. With nearly 39,000 km

The state of California, United States of America produces many crop products that are both utilized domestically and exported throughout the world. With nearly 39,000 km2 of croplands, monitoring unintentional and intentional surface water inundation is important for water resource management and flood hazard readiness. We examine inundation dynamics in California croplands from 2003 to 2020 by intersecting monthly surface water maps (n = 216 months) derived using two satellite remote sensing platforms (Landsat and Moderate Resolution Imaging Spectroradiometer [MODIS]) with a high-quality cropland map generated by the California Department of Water Resources. Surface water maps were produced using the Dynamic Surface Water Extent model, in which satellite image pixels are classified into different levels of detection confidence. Our analysis focused on calculating monthly and annual occurrence of “high confidence” water for each satellite collection across eight cropland types and 58 counties. Results indicate that 49.9% (MODIS) to 56.4% (Landsat) of croplands were inundated at least once during the 18-year timespan. Rice crops, due to their unique need of consistent surface water and dominance as a crop type in CA, had the highest proportion of and mean annual inundation area, while citrus crops had the lowest. Mean monthly inundation patterns in most croplands followed California's precipitation patterns with high inundation during the winter and spring rainy season. At the county level, croplands in the southern Central Valley typically had high occurrences of inundation in conjunction with large crop areas. Exposure and sensitivity of inundation for three crop types (citrus, deciduous, and vineyards) that are typically less associated with intentional inundation were geographically variable, but overall were generally highest in counties in the southern Central Valley, California's primary agricultural region. Flood and precipitation related crop insurance claims indicated that rice had the highest mean indemnity payout for any month with damages typically occurring in March and April. Insurance claims were also high in deciduous fruit and nut crops, which had peak damages in February. A comparison between inundation results and insurance claims suggests that the inundation mapped by our process coincides with claim activity. These data elucidate water inundation patterns across the state that can serve to inform farmers, insurers, decision makers, resource managers, and flood mitigation professionals.

Using the Distinct Population Segment concept to protect fishes with low levels of genomic differentiation: conservation of an endemic minnow (Hitch, Lavinia exilicauda)

American Fisheries Society (AFS) | December 23rd, 2018

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species that are endangered or threatened throughout all or a portion of their rang

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species that are endangered or threatened throughout all or a portion of their range. The definition of “species” includes subspecies and distinct population segments (DPSs). Among freshwater fishes, the use of DPS designations has largely been restricted to salmonids, although the DPS concept is increasingly applied to other fishes as well. As more taxa approach threatened status, the difficult question becomes what to do when genetic evidence does not strongly support formal taxonomic designations (full species or subspecies). We examine the potential application of the DPS concept to protect fishes by using the example of the Hitch Lavinia exilicauda, a cyprinid fish that is endemic to California. The Hitch is divided into three formally described, geographically separate subspecies (the Sacramento, Monterey, and Clear Lake Hitches). However, genomic studies (i.e., restriction site‐associated DNA sequencing), presented here with three independent analyses using a large data set, only weakly supported subspecies designations. Results suggested population structure but not subspecies structure. Nevertheless, conventional taxonomic methods, strong contemporary isolation, the importance of protecting genetic diversity, and high cultural value still qualify all three designated subspecies for DPS status and demonstrate how taxa such as the Clear Lake Hitch can warrant protection under the ESA.

Valuing the benefits of forest restoration on enhancing hydropower and water supply in California's Sierra Nevada

Science of the Total Environment (Elsevier) | March 15th, 2023

Forest restoration through mechanical thinning, prescribed burning, and other management actions is vital to improving forest resilience to fire and drought across the We

Forest restoration through mechanical thinning, prescribed burning, and other management actions is vital to improving forest resilience to fire and drought across the Western United States, and yields benefits that can be monetized, including improvements in water supply and hydropower. Using California's Sierra Nevada as a study area, we assess the water and energy benefits of forest-restoration projects. By using a scalable top-down approach to track annual evapotranspiration following forest disturbance, coupled with hydropower simulations that include energy-price information, and marginal prices for water sales, we project the potential economic benefits of hydropower and water sales accruing to water-rights holders. The results found that water-related benefits from strategically planned fuels-reduction treatments now being carried out can be sufficient to offset costs of management actions aimed at forest restoration, especially in the face of climate change. Our findings justified investments in restoring forests and reinforce the central role of water and hydropower providers in partnerships for management of source-water watersheds. Results also highlighted the importance of accurate, scalable data and tools from the hydrology and water-resources community.

Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act

National Marine Fisheries Service (NMFS) | July 25th, 2016

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five ye

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five years and determine whether any species should be removed from the list or have its listing status changed. Assessments of the viability of ESA-listed Pacific salmonids were conducted by the Southwest Fisheries Science Center and the Northwest Fisheries Science Center. The information from these assessments is incorporated into the West Coast Region’s status review, and the NMFS West Coast Region will make final determinations about any proposed changes in listing status, taking into account not only biological information (viability assessments) but also threats to the species and ongoing or planned protective efforts. This report from the Southwest Fisheries Science Center covers 10 ESA-listed Evolutionarily Significant Units (ESUs) and Distinct Population Segments (DPSs) that lie wholly or partially in California. In this review, we consider 1) new information relevant to the delineation of ESU/DPS boundaries, and 2) new information on status and trends in abundance, productivity, spatial structure and diversity specifically addressed by viability criteria previously developed by Technical Recovery Teams (TRTs). These viability assessments summarize current information (through the 2014–2015 spawning year where available) with respect to the viability criteria developed by the TRTs.  Consequently, the current assessments consider not only changes in populations that have occurred since the 2010 assessments but also the status of populations and ESUs/DPSs in relation to the viability criteria developed by the TRTs. For eight of the ESUs/DPSs (Southern Oregon/Northern California Coho Salmon, Central California Coast Coho Salmon, California Coastal Chinook Salmon, Northern California Steelhead, Central California Coast Steelhead, South-central California Steelhead, Southern California Steelhead, and California Central Valley Steelhead) the new information suggests that there has been no change in extinction risk since 2010 viability assessments. For two ESUs (Central Valley Spring-run Chinook Salmon, and Sacramento River Winter-run Chinook Salmon) the new information suggests a change in extinction risk. The viability of Central Valley Spring-run Chinook salmon appears to have improved since the 2010 assessment, but this ESU is far from being viable and is still facing relatively high extinction risk. The viability of Sacramento River Winter-run Chinook Salmon has been reduced and the ESU faces greater extinction risk since the 2010 assessment.

Vina Groundwater Subbasin Groundwater Sustainability Plan

Vina and Rock Creek Reclamation District Groundwater Sustainability Agencies | December 15th, 2021

The Vina GSA and Rock Creek Reclamation District GSA and the stakeholders within the Subbasin recognize that this GSP is not the finish line; it is the starting line for

The Vina GSA and Rock Creek Reclamation District GSA and the stakeholders within the Subbasin recognize that this GSP is not the finish line; it is the starting line for sustainable management of the Subbasin. As conditions within the Subbasin change, the GSAs within the Subbasin are committed to an open, transparent, and all-inclusive adaptive management strategy aimed at tackling the important local issues that they face. At the heart of SGMA is the power for locals to solve local problems with local resources. All parties in the Subbasin are committed to doing just that.

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.

Water Accounting in Western US, Australia, and Spain: Comparative Analysis

American Society of Civil Engineers (ASCE) | January 10th, 2020