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Open Access Publications from the University of California

Technical Completion Reports

The Water Resources Center (WRC) engages the resources of the University of California with other institutions in the state for the purpose of developing ecologically-sound and economically efficient water management policies and programs in California. The WRC fulfills this mission by stimulating and supporting water-related research and education activities among the various academic departments and research organizations of the university through grants. It collects historic and other documents related to water topics through the Archives and makes the collection available to the public.

Cover page of Climate Variability of the Sierra Nevada Over the Last Millennium: Reconstructions from Annually Laminated Sediments in Swamp Lake, Yosemite National Park, CA

Climate Variability of the Sierra Nevada Over the Last Millennium: Reconstructions from Annually Laminated Sediments in Swamp Lake, Yosemite National Park, CA


Persistent drought presents one of the greatest risks of climate change faced by the western United States. Highlighting this risk is from paleo hydrological evidence that during the medieval period (~900-1400 AD) this region experienced two extensive droughts of greater duration than any experienced in recorded history. However, much remains to be learned about these “mega droughts,” including the severity of deficit in precipitation and snowpack in California’s Sierra Nevada Mountain range, which currently serve as a crucial source of fresh water to California agriculture, industry and domestic users. To possibly extract a record of the hydrological conditions in the Sierra Nevada during this era, cores of annually laminated sediment from Swamp Lake, in the northwest portion of Yosemite Park were collected. Stable hydrogen isotope (δD) ratios of plant leaf-wax lipid compounds preserved in the lake sediments and the thickness of the annual sedimentary laminations (varves) show promise as potential proxies for recording past hydroclimate variability in the Sierra Nevada Mountains. δD measurements at annual to interannual resolution were made for two time periods: the 20th century and the 13th-15th centuries while varve thickness was measured over the entire period 1150-2006 AD. We find significant negative correlations between 20th century δD fluctuations and instrumentally recorded variability in total precipitation, snow water equivalence (SWE) and Palmer Drought Severity Index (PDSI). Medieval δD values correspond to independent regional hydrologic reconstructions at the decadal to multi-decadal scale, which appear to delineate relatively dry medieval episodes. An issue that is still unclear is that the mean δD during this period is little different from that during the relatively moist contemporaneous period. This finding is at odds with evidence from submerged tree stumps for two prolonged droughts separated by about 200 years. Varve thickness measurements are on going, but results thus far reveal difficulties in using this proxy for reconstructing past Sierra Nevada hydroclimate variability, the most significant being the complexity of the seasonal deposition cycle and sub-millimeter thicknesses. Overall, geochemical and geomorphological information gleaned from Swamp Lake sediment cores provide an independent means of reconstructing hydroclimate in the Sierra Nevada and provide a unique perspective on the mega-drought intervals in the Sierra Nevada Mountains.

Cover page of Enforcement-driven financing of water quality in California: The case of supplemental environmental projects

Enforcement-driven financing of water quality in California: The case of supplemental environmental projects


In this report, we compile empirical evidence regarding federal and state trends in the use of Supplemental Environmental Projects (SEPs). Our primary interest is in SEPs associated with enforcement of the federal Clean Water Act (CWA). We move from briefly examining the broadest trends—federal and state use of SEPs—to more particular emphasis on the experience of California’s State Water Resources Control Board (SWRCB) and Regional Water Quality Control Boards (RWQCB) with SEPs. Drawing on state and regional enforcement databases as well as extensive interviews with agency enforcement personnel, we evaluate the use of SEPs by the regional boards in California and offer recommendations for improving the use of this important policy tool.

Cover page of Simulating and understanding variability in runoff from the Sierra Nevada

Simulating and understanding variability in runoff from the Sierra Nevada


We have conducted a study of Sierra Nevada runoff by analyzing the onset of snowmelt (or peak snowmass timing) from observations and conducting model simulations of snowpack. For our observation study, monthly snow water equivalent (“SWE”) measurements were combined from two data sets to provide sufficient data from 1930 to 2008. The monthly snapshots are used to calculate peak snow mass timing for each snow season. Since 1930, there has been an overall trend towards earlier snow mass peak timing by 0.6 days per decade. The trend towards earlier timing also occurs at nearly all individual stations. Even stations showing an increase in April 1st SWE exhibit the trend toward earlier timing, indicating that enhanced melting is occurring at nearly all stations. Analysis of individual years and stations reveals that warm daily maximum temperatures averaged over March and April are associated with earlier snow mass peak timing for all spatial and temporal scales included in the data set. The influence is particularly pronounced for low accumulation years indicating the potential importance of albedo feedback for the melting of shallow snow. The robustness of the early spring temperature influence on peak timing suggests the trend towards earlier peak timing is attributable to the simultaneous warming trend (0.1ºC per decade since 1930, with an acceleration in warming in later time periods). For our modeling study, we have used the Weather Research and Forecasting Model (“WRF”) to model snowpack at high resolution over the Sierra Nevada during the 2001-2002 water year. We have focused on one year to validate the use of WRF for understanding runoff variability. We have found that high resolutions are necessary to accurately model snow cover over the Sierras.

Cover page of Integrated regional water management: Collaboration or water politics as usual?

Integrated regional water management: Collaboration or water politics as usual?


This report analyzes the effectiveness of integrated regional water management (IRWM) in the San Francisco Bay-Area of California for decreasing fragmentation and increasing collaboration among water management stakeholders. The theory identifies the elements of traditional water management politics that lead to fragmentation and conflict. The water-politics-as-usual model is then compared to the collaborative model of integrated water management. The evolution of IRWM in California is briefly described. A survey of Bay Area stakeholders is used to assess whether participation in the Bay Area IRWM achieves the goals of collaboration and integration. The basic results suggest the Bay Area has made only incremental progress away from the fragmentation and conflict seen in the past.

Cover page of Maintenance and Dissemination of a Water Transfer Data Base for 12 Western States, 1987-2008

Maintenance and Dissemination of a Water Transfer Data Base for 12 Western States, 1987-2008


The project involves collaborate work between Gary Libecap and a graduate student, Zachary Donohew, to compile and maintain a comprehensive, publiclyavailable data set on water transfers and water markets for researchers and policy analysts. The data are drawn from the Water Strategist for 12 western states (Washington, Oregon, California, Arizona, Nevada, Utah, Idaho, Montana, Wyoming, Colorado, New Mexico and Texas) from January 1987-December 2008. There are 4,175 observations of water transfers that include amount of water, contract type (short-term lease, long-term lease, and sale), parties involved, origination use, destination use, and price (2,728 observations). The methodology is described and data categories are presented in a Word document along with an excel file of the trades placed on the Bren School Website and linked to the Bren website at and the WRRC website at

Cover page of Assessment of Seawater Intrusion Potential From Sea-level Rise in Coastal Aquifers of California

Assessment of Seawater Intrusion Potential From Sea-level Rise in Coastal Aquifers of California


The California Department of Water Resources (2006) estimated a rise in mean sea level along California’s coastline ranging from 10 to 90 cm over the 21st century due to rising global mean surface temperature. This range of sea-level rise is consistent with the Intergovernmental Panel for Climate Change (2007) estimates. The rise in sea level threatens coastal aquifers by exacerbating the risk of saline intrusion. This study simulated the effect of sea-level rise on the Seaside Area sub-basin near the City of Monterey, California. The simulation was carried out with a state-of-art, finite-element, variable-density, numerical model that accounts for the effects of salinity on groundwater density and viscosity. Seawater intrusion was simulated for various scenarios of sea-level rise, varying from 0 m to 1 m assuming a linear increase of sea level through the 21st century. Each scenario contemplated the same level of predicted groundwater extraction through the 21st century in the study aquifers. The numerical simulations of seawater intrusion indicate that one meter of sea-level rise would contribute an additional 10 to 15 meters of inland spread of the 1,000 mg/L saline front and 20 to 30 meters of the 10,000 mg/L saline front. The effect of sea-level rise on seawater intrusion in the Seaside Area sub-basin, therefore, appears minor when compared with historical measurements of seawater intrusion caused primarily by groundwater pumping since the early 1900s. Other aquifers with less topographical relief and more complex hydrostratigraphy could be more vulnerable to sea-level rise, however. One such possibility is posed by the Oxnard Plain groundwater sub-basin, in Ventura County, California. This study compiled a hydrogeologic database and structured the basic elements of a sea-water intrusion numerical simulation model for the Oxnard Plain aquifer. The Oxnard Plain sub-basin is a complex, multi-formation, aquifer that has undergone several decades of groundwater extraction, and, which is known to experience seawater intrusion in several of its coastal areas. The Oxnard Plain sub-basin features an important offshore hydrogeologic section that encompasses its boundary under seawater. Time limitations prevented calibration and validation of the numerical simulation model for seawater intrusion in the Oxnard Plain sub-basin. Nevertheless, the elements needed to complete the Oxnard Plain sub-basin’s seawater-intrusion simulation model in the near future (with additional funding) have been assembled and are presented in this report. The approach presented in this report for the relatively assessment of groundwater extraction and sea-level rise effects on seawater intrusion into coastal aquifers holds potential for wide-ranging applicability in a variety of hydrogeologic settings. In particular, the finite-element spatial grid provides distinct capabilities to represent accurately the geographical layout of an aquifer.

Cover page of Sustainable Eco-Systems under Land Retirement

Sustainable Eco-Systems under Land Retirement


This study uses five years of field data from the Land Retirement Demonstration Project located in western Fresno County of California to develop a comprehensive theoretical and numerical modeling framework to evaluate the specific site conditions required for a sustainable land retirement ecosystem outcome based on natural drainage. Using field data, principles of mass balance in a control volume, the HYDRUS-1D Software Package for simulating one-dimensional movement of water, heat, and multiple solutes in variably-saturated media, and PEST, a modelindependent parameter optimizer, the processes of soil water and solute movement in root zone and the deep vadose zone were investigated. The optimization of unsaturated soil hydraulic parameters and downward flux (natural drainage) from the control volume against observed vadose zone salinity levels and shallow groundwater levels yield difficult to obtain natural drainage rate as a function of water table height within the control volume. The results show that unsaturated soil hydraulic properties and the downward flux from the soil profile are the critical parameters. A ‘natural drainage approach’ to sustainable land management for drainage impaired land is proposed. With this approach it is feasible to design a sustainable land use regimen for drainage impaired lands in general and retired lands in particular.

Further analysis of data on the evolution of vadose zone salinity and perched water levels also show that effective unsaturated soil hydraulic property and the "natural drainage rate" change with average soil water salinity. The results show that at the same pressure head, soil water content is less with higher soil water salinity as compared to lower soil water salinity. It is thus concluded that the use of soil water salinity invariant soil water hydraulic parameters in numerical modeling can seriously compromise prediction, especially for a variable soil water salinity environment.

Cover page of Inter-relationships between the spawning migration of Eagle Lake rainbow trout, streamflow, snowpack, and air temperature

Inter-relationships between the spawning migration of Eagle Lake rainbow trout, streamflow, snowpack, and air temperature


Pine Creek has historically provided critical spawning and rearing habitat for Eagle Lake rainbow trout (ELRT, Oncorhynchus mykiss aquilarum). Over the past 100+ years modifications of Pine Creek watershed (e.g., overgrazing, timber harvest, passage barriers, culverts) decoupled the ELRT from its stream habitat. Introduced brook trout (Salvelinus fontinalis) now dominate historic rearing areas in the upper watershed. Passage barriers were constructed on Eagle Lake tributaries to prevent ELRT from spawning in degraded habitat, denying the ELRT access beyond the first kilometer of stream. Since 1950 the lake fishery has been maintained by artificial spawning. Offspring are reared in hatcheries and released into Eagle Lake. Since 1987 changes in grazing management, reconstruction of culverts, and other conservation projects have resulted in marked improvement of habitat, although ELRT have been not allowed to attempt their natural spawning migration. Their ability to migrate has been questioned, and concerns led to a petition for listing under the federal Endangered Species Act. We report on a long term study to track the spring migration of ELRT spawners in Pine Creek. We tracked the upstream migration of ELRT spawners from the mouth of Pine Creek. We then related ELRT spawner migration to stream flow and snowpack, and related flows to snowpack and air temperature. It is possible to predict ELRT migration distance from flow, duration of flow, or from snowpack. The relationships between migration distance and flow, and migration distance and snowpack in the upper watershed were weak. However, sample sizes were small, due to the limited number of years in which fish have been tracked, and the cessation of operation of the flow gages. The positive relationships between migration distance and seasonal average daily mean streamflow, and between streamflow and snowpack are particularly interesting in light of climate predictions for California. By the end of this century snowpack is likely to be reduced 65-97% in the elevation range of Pine Creek. The creek is likely to flow more during the winter, due to winter rain events, and to have lower summer baseflows. It is possible that ELRT spawners might shift to a strategy of earlier migration, moving upstream to areas of perennial summer flow during winter rain events. However, the fish currently lack the opportunity to experience and adapt to flow changes that are likely to occur with climate change.

Cover page of Pyrethroid pesticide transport into Monterey Bay through riverine suspended solids

Pyrethroid pesticide transport into Monterey Bay through riverine suspended solids


The three largest coastal rivers discharging to Monterey Bay, the Salinas, Pajaro, and San Lorenzo Rivers potentially serve as a route of transport of pyrethroids and other pesticides into the shelf waters of Monterey Bay and deeper areas within Monterey Canyon. Suspended sediment samples from the lower reaches of the rivers were collected over several rain events in the winters of 2007/2008 and 2008/2009, and analyzed for pyrethroids and one organophosphate pesticide. Bed sediments from Elkhorn Slough, Monterey Bay, and Monterey Canyon were also analyzed for these same substances. Nearly all suspended sediments contained measurable pyrethroids, with the pyrethroids bifenthrin and permethrin being the most commonly detected. The differences in pyrethroid composition between the rivers, some with predominantly an agricultural watershed and some with substantial urban influence, were relatively minor reflecting the broad uses for many of the insecticides within this class. While it is clear that all three coastal rivers are introducing substantial amounts of pyrethroids into coastal waters, there is sufficient degradation and/or dilution with uncontaminated material such that bed sediments in Monterey Bay and Monterey Canyon contained no quantifiable pyrethroids. Toxicity to sensitive invertebrates due to pyrethroids is likely in the bed sediments of the lower reaches of the Salinas River, and potentially the other rivers, but pyrethroid-related toxicity is not likely in Elkhorn Slough or adjacent coastal waters.

Cover page of Control of mercury methylation in wetlands through iron addition

Control of mercury methylation in wetlands through iron addition


The San Francisco Bay-Delta System lost an estimated 85-95% of its historical tidal marshes to urban development, agriculture, and commercial salt production since the middle of the nineteenth century. Fortunately, there are many recent initiatives underway throughout the estuary to re-establish the important ecosystem functions and critical wildlife habitat that these tidal wetlands offer. However, there is a significant potential drawback to these restorations, as wetlands have been shown to play a major role in the production and export of methylmercury (MeHg), which is a potent neurotoxin that affects both humans and wildlife. While mercury pollution is a global problem, it is of special concern in the San Francisco Bay-Delta, where substantial additional inputs of inorganic mercury from historical mining activities have resulted in increased mercury levels in ecosystem. The potential exacerbation of MeHg health effects due to wetland restoration and construction is a serious concern that has been recognized in recent mercury regulations. However, restoration and management technologies have not yet been developed to control MeHg production and export from wetlands. The research described in this report tested the efficacy of one such potential control: the application of an iron sediment amendment to tidal wetland microcosms.

The conversion of inorganic mercury to MeHg is predominantly a biologically-driven process under typical wetland sediment conditions. The net production of MeHg is controlled by both bacterial activity and the bioavailability of inorganic mercury species to the microbial community. Under the reducing conditions typical of wetland sediments, dissolved mercury speciation and concentration is controlled by the presence of reduced sulfur, and it has been hypothesized that it is the uncharged dissolved Hg-S species that are readily available for methylation, as they are the species able to diffuse into bacterial cells. In this research, we tested the hypothesis that amending wetland sediments with iron will reduce net methylmercury production by decreasing dissolved porewater sulfide concentrations through the formation of insoluble iron-sulfur minerals, which correspondingly decreases the pool of mercury available to the methylating bacteria.

Two laboratory microcosm experiments were conducted using in-tact sediment cores collected from a tidal salt marsh in the San Francisco Bay estuary, where one experiment used sediments that had the vegetation removed and the second included live wetland plants. Microcosms in the devegetated experiment were split into four dosing groups (0, 180, 360, and 720 g- Fe/m2) and were monitored for a period of 17 weeks. Shortly after iron addition, porewater S(-II) concentrations decreased significantly at all iron doses relative to the control, and net MeHg production and export to the overlying surface water decreased by over 90% at the highest iron doses. Despite some conversion of FeS(s) to pyrite, the effects persisted for at least 12 weeks. The inclusion of wetland vegetation substantially increased the amount of variation between triplicate cells, but general trends were similar to those found in the devegetated experiment.

This project was the first work to demonstrate that an iron sediment amendment has the potential to be an effective control of methylmercury production in tidal wetland sediments at the microcosm scale. These results have laid the groundwork for future studies to evaluate the efficacy of an iron amendment at the field scale, which could demonstrate that this technique is a viable landscape-scale control on methylmercury production in restored and constructed tidal wetlands.