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The 178,000-acre Grassland Ecological Area in California’s San Joaquin Valley is managed to provide overwintering habitat to waterfowl on the Pacific Flyway. The major management activity is the fall flooding and spring drawdown of wetlands, timed to optimize the availability of forage vegetation and invertebrates for ducks and shorebirds. Wetland drainage contains salt, boron, and trace elements that are largely derived from imported surface water but concentrate during storage in the wetland impoundments and contribute to occasional water quality violations in the San Joaquin River (SJR) during dry years. Compliance with water quality objectives may be improved by timing wetland drawdown to coincide with high SJR salt assimilative capacity during mid-March to mid-April when reservoir releases are increased to aid salmon migration.The experimental sites chosen were three pairs of matched wetland basins (20-100 acres each) that are part of the larger Modified Hydrology Study. For each wetland pair, one was managed with a traditional March drawdown; while the drawdown was delayed up to one month for the other to coincide with the period of high SJR assimilative capacity. Two additional drainage sites were added to the second year of sampling to better characterize drainage flowing to the SJR. Soil and water column samples were collected during the flooded periods at the inlets, outlets, and along transects within the wetlands. Water quality analyses included total/volatile suspended solids, conductivity, nitrogen (NH4+, NO2-+NO3-, organic), phosphorus (total, PO43-), total organic carbon, alkalinity, turbidity, temperature, and pH. Planktonic and benthic invertebrates were identified and enumerated. Data were collected between February and April in 2007 and again in 2008.Identified phytoplankton were predominantly chlorophytes and diatoms. Zooplankton that feed on phytoplankton were found in abundance and consisted mostly of Cladocera. Benthic invertebrate densities were also measured to help explain the differences in algal concentrations between ponds. Benthic invertebrates were found to be predominantly Chironomidae.Seasonal loads of volatile suspended solids, total dissolved solids, and total organic carbon were estimated at the two aggregate drainage sites and at one delayed drawdown wetland during the 2008 season. For volatile suspended solids, the discharged load was 1500 lbs at the Buttonwillow drainage site, 2500 lbs at the Los Banos 38 drainage site, and upstream of those sites, 770 lbs were discharged from the Mud Slough 4b wetland. For total dissolved solids, the discharged load was 293 tons, 524 tons, and 26 tons, respectively, for the same locations.Of the factors potentially limiting phytoplankton concentrations, invertebrate grazing was likely the most important. Nutrients were not limiting in either the traditional or modified wetlands, as indicated by sufficient N and P content in the algae biomass. Likewise, inorganic C was not limiting, as indicated by pH (most

San Luis National Wildlife Refuge Complex to meet Reclamation s obligations for Level 4 water supply under the Central Valley Project Improvement Act. Hydrogeological assessment of the East Bear Creek Unit of the San Luis National Wildlife Refuge was conducted using a combination of field investigations and a survey of available literature from past US Geological Survey Reports and reports by local geological consultants. Conservative safe yield estimates made using the available data show that the East Bear Creek Unit may have sufficient groundwater resources in the shallow groundwater aquifer to meet about between 25 percent and 52 percent of its current Level II and between 17 percent and 35 percent of its level IV water supply needs. The rate of surface and lateral recharge to the Unit and the design of the well field and the layout and capacity of pumped wells will decide both the percentage of annual needs that the shallow aquifer can supply and whether this yield is sustainable without affecting long-term aquifer quality. In order to further investigate the merits of pumping the near surface aquifer, which appears to have reasonable water quality for use within the East Bear Creek Unit -- monitoring of the potential sources of aquifer recharge and the installation of a pilot shallow well would be warranted. Simple monitoring stations could be installed both upstream and downstream of both the San Joaquin River and Bear Creek and be instrumented to measure river stage, flow and electrical conductivity. Ideally this would be done in conjunction with a shallow pilot well, pumped to supply a portion of the Unit's needs for the wetland inundation period.

This project deliverable describes a number of state-of-the-art, telemetered, flow and water quality monitoring stations that were designed, instrumented and installed in cooperation with local irrigation water districts to improve water quality simulation models of the lower San Joaquin River, California. This work supports a multi-disciplinary, multi-agency research endeavor to develop a science-based Total Maximum Daily Load for dissolved oxygen in the San Joaquin River and Stockton Deep Water Ship Channel.

Seasonally managed wetlands in the Grasslands Basin of California's San Joaquin Valley provide food and shelter for migratory wildfowl during winter months and sport for waterfowl hunters during the annual duck season. Surface water supply to these wetland contain salt which, when drained to the San Joaquin River during the annual drawdown period, negatively impacts downstream agricultural riparian water diverters. Recent environmental regulation, limiting discharges salinity to the San Joaquin River and primarily targeting agricultural non-point sources, now addresses return flows from seasonally managed wetlands. Real-time water quality management has been advocated as a means of matching wetland return flows to the assimilative capacity of the San Joaquin River. Past attempts to build environmental monitoring and decision support systems to implement this concept have failed for reasons that are discussed in this paper. These reasons are discussed in the context of more general challenges facing the successful implementation of environmental monitoring, modelling and decision support systems. The paper then provides details of a current research and development project which will ultimately provide wetland managers with the means of matching salt exports with the available assimilative capacity of the San Joaquin River, when fully implemented. Manipulation of the traditional wetland drawdown comes at a potential cost to the sustainability of optimal wetland moist soil plant habitat in these wetlands - hence the project provides appropriate data and a feedback and response mechanism for wetland managers to balance improvements to San Joaquin River quality with internally-generated information on the health of the wetland resource. The author concludes the paper by arguing that the architecture of the current project decision support system, when coupled with recent advances in environmental data acquisition, data processing and information dissemination technology, holds significant promise to address some of the problems described earlier in the paper that have limited past efforts to improve Basin water quality management.

Hydrogeological assessment of the 4-S Land and Cattle Company (4-S Ranch) was conducted using a combination of field investigations and a survey of available literature from nearby agricultural water districts and other entities. The 4-S Ranch has been able to meet most of its own water needs providing irrigated pasture for beef cattle by an active program of shallow groundwater pumping in the semiconfined aquifer above the Corcoran Clay. Comparison of groundwater pumping on the 4-S Ranch property with groundwater pumping in the adjacent Merquin and Stevinson Water Districts shows great similarity in the well screened depths and the quality of the groundwater produced by the well fields. The pump yield for the eight active production wells on the 4-S property are comparable to the production and drainage wells in the adjacent water districts. Like these Districts the 4-S Ranch lies close to the Valley trough in a historic discharge area. The 4-S Ranch is unique in that it is bounded and bisected by several major water conveyance facilities including Bear Creek. Although the large number of potential recharge structures would suggest significant groundwater conjunctive use potential the major well field development has occurred along the length of the Eastside Canal. The Eastside Canal is known to be leaky above the "A" Clay the Canal passes through sandy areas and experiences significant groundwater seepage. This seepage can be intercepted by adjacent groundwater wells. Pumping adjacent to, and along the alignment of the Canal, may induce higher rates of seepage from the Eastside Canal. Groundwater quality below and adjacent to the Eastside Canal is very good, reflecting the origin of this diverted water from the Merced River. Most of the pumpage occurs in a depth interval between 30 ft and 130ft. Safe yield estimates made using the available data show that the 4-S Ranch has sufficient resources to meet its own needs. Further exploitation of the groundwater will be limited if the leakage from the Eastside Bypass, Mariposa Bypass and Bear Creek are insufficient to replace the pumped water on an average annual basis. Should any future lining of the Eastside Canal occur, it would have a significant impact on the groundwater resource potential of the 4-S Ranch and impair the overall quality of the available water supply.

Salt management has been a challenge to westside farmers since the rapid expansion of irrigated agriculture in the 1900 s. The soils in this area are naturally salt-affected having formed from marine sedimentary rocks rich in sea salts rendering the shallow groundwater, and drainage return flows discharging into the lower reaches of the San Joaquin River, saline. Salinity problems are affected by the imported water supply from Delta where the Sacramento and San Joaquin Rivers combine. Water quality objectives on salinity and boron have been in place for decades to protect beneficial uses of the river. However it was the selenium-induced avian toxicity that occurred in the evaporation ponds of Kesterson Reservoir (the terminal reservoir of a planned but not completed San Joaquin Basin Master Drain) that changed public attitudes about agricultural drainage and initiated a steady stream of environmental legislation directed at reducing non-point source pollution of the River. Annual and monthly selenium load restrictions and salinity and boron Total Maximum Daily Loads (TMDLs) are the most recent of these policy initiatives. Failure by both State and Federal water agencies to construct a Master Drain facility serving mostly west-side irrigated agriculture has constrained these agencies to consider only In-Valley solutions to ongoing drainage problems. For the Westlands subarea, which has no surface irrigation drainage outlet to the San Joaquin River, innovative drainage reuse systems such as the Integrated Farm Drainage Management (IFDM) offer short- to medium-term solutions while more permanent remedies to salt disposal are being investigated. Real-time salinity management, which requires improved coordination of east-side reservoir releases and west-side drainage, offers some relief to Grasslands Basin farmers and wetland managers - allowing greater salinity loading to the River than under a strict TMDL. However, current regulation drives a policy that results in a moratorium on all drainage return flows.

In the past decade tens of millions of dollars have been spent by water resource agencies in California to restore the native salmon fishery in the San Joaquin River and its major tributaries. An excavated deep water ship channel (DWSC), through which the river runs on its way to the Bay/Delta and Pacific Ocean, experiences episodes of low dissolved oxygen which acts as a barrier to anadromous fish migration and a threat to the long-term survival of the salmon run. An emergency response management system is under development to forecast these episodes of low dissolved oxygen and to deploy measures that will raise dissolved oxygen concentrations to prevent damage to the fishery resource. The emergency response management system has been designed to interact with a real-time water quality monitoring network and is served by a comprehensive data management and forecasting model toolbox. The Bay/Delta and Tributaries (BDAT) Cooperative Data Management System is a distributed, web accessible database that contains terabytes of information on all aspects of the ecology of the Bay/Delta and upper watersheds. The complexity of the problem dictates data integration from a variety of monitoring programs. A unique data templating system has been constructed to serve the needs of cooperating scientists who wish to share their data and to simplify and streamline data uploading into the master database. In this paper we demonstrate the utility of such a system in providing decision support for management of the San Joaquin River fishery. We discuss how the system might be expanded to have further utility in coping with other emergencies and threats to water supply system serving California's costal communities.

The project report describes a two year experiment to control wetland drainage to the San Joaquin River of California from the San Luis National Wildlife Refuge using a decision support system for real-time water quality management. This system required the installation and operation of one inlet and three drainage flow and water quality monitoring stations which allowed a simnple mass balance model to be developed of the seasonally managed wetlands in the study area. Remote sensing methods were developed to document long-term trends in wetland moist soil vegetation and soil salinity in response to management options such as delaying the initiation of seasonal wetland drainage. These environmental management tools provide wetland managers with some of the tools necessary to improve salinity conditions in the San Joaquin River and improve compliance with State mandated salinity objectives without inflicting long-term harm on the wildfowl habitat resource.

The purpose of the research project was to advance the concept of real-time water quality management in the San Joaquin Basin by developing an application to drainage of seasonal wetlands in the Grassland Water District. Real-time water quality management is defined as the coordination of reservoir releases, return flows and river diversions to improve water quality conditions in the San Joaquin River and ensure compliance with State water quality objectives. Real-time water quality management is achieved through information exchange and cooperation between shakeholders who contribute or withdraw flow and salt load to or from the San Joaquin River. This project complements a larger scale project that was undertaken by members of the Water Quality Subcommittee of the San Joaquin River Management Program (SJRMP) and which produced foreca sts of flow, salt load and San Joaquin River assimilative capacity between 1999 and 2003. These forecasts can help those entities exporting salt load to the River to develop salt load targets as a mechanism for improving compliance with salinity objectives. The mass balance model developed by this project is the decision support tool that helps to establish these salt load targets. A second important outcome of this project was the development and application of a methodology for assessing potential impacts of real-time wetland salinity management. Drawdown schedules are typically tied to weather conditions and are optimized in traditional practices to maximize food sources for over-wintering wildfowl as well as providing a biological control (through germination temperature) of undesirable weeds that compete with the more proteinaceous moist soil plants such as swamp timothy, watergrass and smartweed. This methodology combines high resolution remote sensing, ground-truthing vegetation surveys using established survey protocols and soil salinity mapping using rapid, automated electromagnetic sensor technology. This survey methodology could be complemented with biological surveys of bird use and invertebrates to produce a robust long-term monitoring strategy for habitat health and sustainability.

This wetland plant guide was developed to aid moist soil plant identification and to assist in the mapping of waterfowl and shorebird habitat in the Grassland Water District and surrounding wetland areas. The motivation for this habitat mapping project was a concern that real-time salinity management of wetland drainage might have long-term consequences for wildfowl habitat health -- changes in wetland drawdown schedules might, over the long term, lead to increased soil salinity and other conditions unfavorable to propagation of the most desirable moist soil plants. Hence, the implementation of a program to monitor annual changes in the most common moist soil plants might serve as an index of habitat health and sustainability. Our review of the current scientific and popular literature failed to identify a good, comprehensive field guide that could be used to calibrate and verify high resolution remote sensing imagery, that we had started to use to develop maps of wetland moist soil plants in the Grassland Water District. Since completing the guide it has been used to conduct ground truthing field surveys using the California Native Plant Society methodology in 2004. Results of this survey and a previous wetland plant survey in 2003 are published in a companion LBNL publication summarizing 4 years of fieldwork to advance the science of real-time wetland salinity management.

The electrical conductivity profiles recorded in a well using the flowing fluid electric conductivity (FEC) logging method can be analyzed to estimate interval-specific hydraulic conductivity and estimates of the salinity concentration with depth. A study demonstrates that a modified, miniaturized FEC logging system can be successfully used in irrigation wells with limited access and large diameters.