San Joaquin River

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 machine learning to predict 1,2,3-trichloropropane contamination from legacy non-point source pollution of groundwater in California's Central Valley

Elsevier | May 6th, 2023

1,2,3-tricholoropropane (TCP) is an impurity common in nematicides applied to agricultural soils from the 1940s to the 1980s. Evidence from animal studies indicates t

1,2,3-tricholoropropane (TCP) is an impurity common in nematicides applied to agricultural soils from the 1940s to the 1980s. Evidence from animal studies indicates that TCP is a probable human carcinogen. TCP leaches through the soil into groundwater where it persists and contaminates thousands of wells in Asia, Europe, and North America. In California, TCP contaminates drinking water wells, with the highest levels of TCP beneath agricultural land used to grow grapevines. This study performs a mass balance and evaluates the ability of three types of tree-based machine learning models to predict TCP concentration in California's Central Valley aquifer system: classification and regression trees (CART), Random Forest (RF), and Boosted Regression Trees (BRT). To construct the models, multiple spatial explanatory variables were used, including historical agricultural land use data, irrigation levels, precipitation, soil type, groundwater age, redox state, and the presence of the co-contaminant nitrate. To estimate the amount of TCP applied to farmland in California, state historical pesticide and land use documents were used in the mass balance. Between 110,000 and 4,300,000 kg of TCP are estimated to have accumulated in the subsurface. Machine learning models indicate that the most important explanatory variables to predict TCP contamination of groundwater are precipitation, redox state, and the presence of the co-contaminant nitrate. Additionally, a 1000-m buffer area offers a slightly higher predictive performance as compared to 500-m and 1500-m buffers. Furthermore, the RF model outperforms CART and BRT for predictive performance. Finally, modeling using decision trees can predict TCP contamination levels in areas where monitoring is lacking, help target future TCP monitoring efforts, and aid in identifying areas to avoid when drilling new drinking water wells.

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.

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.

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

Water Allocation in California - Legal Rights and Reform Needs

Golden Gate University (GSU) | March 31st, 1982

FOREWARD: Water supply, allocation, use and conservation are constantly debated in California, often appearing as highly charged political issues in candidates' races and

FOREWARD: Water supply, allocation, use and conservation are constantly debated in California, often appearing as highly charged political issues in candidates' races and on election ballots. This year is no exception, with major ballot propositions already scheduled for the June primary election and being circulated to qualify for the November general election. Accordingly this Research Paper on legal aspects of water allocation is being published for the valuable background it affords readers wishing to learn more about the subject. The author draws on his legal expertise, as well as his experience as Staff Director of the Governor's Commission to Review California Water Rights Law. The paper emphasizes the crucial role of water rights in California water management, and it points to the need for and present lack of a political consensus on water law reform. The author concludes by suggesting forces that could bring about interest-group realignments and other developments favorable to achieving the needed consensus on water law and management reform that so far has eluded Californians. Stanley Scott Assistant Director Institute of Governmental Studies March 1982

Water and Energy in California

Public Policy Institute of California (PPIC) | December 6th, 2022

Water and Suspended-Sediment Flux Measurements at the Golden Gate, 2016-2017

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

Sediment is an important resource for San Francisco Bay (SFB), in the context of restoration projects, dredging operations, ecosystem health, and contaminant transport an

Sediment is an important resource for San Francisco Bay (SFB), in the context of restoration projects, dredging operations, ecosystem health, and contaminant transport and fate. Understanding the transport and fate of sediment in SFB is important to ecosystem researchers and managers. Previous studies have shown that sediment exchange at the estuary-ocean boundary of SFB (Golden Gate inlet) is the most poorly understood element of the SFB sediment budget, owing to logistical challenges that inhibit routine field observations, and the fact that net flux is a small fraction of the instantaneous peak values experienced on a daily basis. Improved understanding of sediment exchange at the estuary-ocean boundary of SFB is essential to updating SFB-wide sediment budgets, which account for sources, sinks, and storage of sediment (and sediment-associated contaminants). In this study, field observations of water and suspended-sediment fluxes at the Golden Gate were made over one ebb tide and one flood tide on three occasions: 1) 21-22 March 2016, following a large storm event that triggered the first flow into Yolo Bypass flood control structure since 2011 2) 23 June of 2016, during a period of low freshwater inflow; 3) 27-28 February 2017, following several large storms of the wettest winter in northern California in recorded history.

Water and the Future of the San Joaquin Valley

Public Policy Institute of California (PPIC) | February 14th, 2019

The San Joaquin Valley—California’s largest agricultural region and an important contributor to the nation’s food supply—is in a time of great change. The valle

The San Joaquin Valley—California’s largest agricultural region and an important contributor to the nation’s food supply—is in a time of great change. The valley is ground zero for many of California’s most difficult water management problems—including groundwater overdraft, drinking water contamination, and declines in habitat and native species. Local water supplies are limited, particularly in the southern half of the region. To irrigate their crops, many farmers use water imported from the Sacramento–San Joaquin Delta. But in many places farmers have also relied on groundwater overdraft—pumping groundwater in excess of the rate at which it is replenished. Worsening droughts, increasing regulations to protect endangered native fishes, and growing demand by Southern California for Delta imports have compounded surface water scarcity. The state’s Sustainable Groundwater Management Act (SGMA) requires local water users to bring groundwater use to sustainable levels by the early 2040s. This will have a broad impact on valley agriculture and the regional economy in coming years—likely including some permanent idling of farmland. This report explores three key challenges facing the San Joaquin Valley and reviews the most promising approaches to address them:  Balancing water supplies and demands. To close the groundwater deficit, groundwater sustainability agencies in the valley’s overdrafted basins will have to augment supplies, reduce demands, or use some combination of these two approaches. A range of options are under consideration but they are not equally effective or practical.  Addressing groundwater quality challenges. Poor groundwater quality impairs drinking water supplies in disadvantaged rural communities, reduces long-term agricultural prosperity, and degrades ecosystems. Providing safe drinking water is an urgent priority. Over the longer term, parties will also need to manage water quantity and quality together, to take advantage of synergies and avoid unintended consequences. The necessary coordination will be challenging because the various programs addressing valley water quality issues are carried out by numerous local and regional entities, whose lines of responsibility and geographic boundaries do not neatly align.  Fostering beneficial water and land use transitions. Effectively addressing water scarcity and the resulting land use changes in the San Joaquin Valley offers opportunities to put lands coming out of production to good use—and gain “more pop per drop” from limited water resources. Multiple-benefit approaches to water and land management can enhance groundwater recharge and improve air and water quality. They can also promote healthier soils, new recreational opportunities, additional flood protection, improved habitat, and new revenue streams for private landowners engaging in conservation-oriented management. Addressing these complex and intertwined issues requires significant changes in water and land management and a major ramp-up in cooperation and coordination among a wide circle of stakeholders. Pursuing solutions that deliver multiple benefits will boost the chances of success overall. The entire region—and California as a whole—will benefit if solutions to these challenges are cost-effective and support the valley’s economy while improving public health and the natural environment.