San Joaquin River Research Articles

Reintroduction of spring‐run Chinook salmon in the San Joaquin River: Evaluating genetic and phenotypic effects of captive breeding

AbstractCaptive‐breeding programs are increasingly implemented to curb population declines but can have unintended negative effects on genetic diversity and phenotypes. Through an analysis of ~10 years of genetic monitoring, pedigree information, and phenotypic data, we evaluated a captive‐breeding program that uses adaptive management to reduce inbreeding and improve captive broodstock performance. A captive‐breeding program was established in 2012 to reintroduce spring‐run Chinook salmon to the southern edge of their range in California's San Joaquin River (SJR), using fish produced each year at the nearby Feather River Hatchery (FRH). We found that the SJR program adequately captured the genetic diversity of the FRH source population and that mate pairings guided by genetic relatedness reduced inbreeding. However, the SJR broodstock reared in captivity had smaller body size at maturity in comparison to the FRH source broodstock which matures at sea, but this effect disappeared when SJR juveniles were released from captivity to mature at sea. Phenotypic traits of SJR female parents also influenced reproductive performance; older mothers and those with smaller eggs had offspring with lower survival. These findings demonstrate that adaptive genetic monitoring and pedigree information can be powerful tools for reducing risks of captive breeding and evaluating program effectiveness.

Simulation of Flow and Salinity in a Large Seasonally Managed Wetland Complex

Seasonally managed wetlands in the San Joaquin River (SJR) watershed in California provide important benefits to wildlife and humans but are threatened through anthropogenic activity. Wetlands in the SJR are subject to salinity regulation, which poses challenges for wetland management. Salinity management in the SJR basin is supported by a process-based model, the Watershed Analysis Risk Management Framework (WARMF). Wetlands are simulated with a “bathtub” analog where water levels are assumed to be the same over one model compartment and the storage volume depends on depth. The complexity and extent of hydrological features pose challenges for input data acquisition. Two approaches to estimating inflow and pond depth and determining water sources were assessed. Approach 1 used mostly monitored data, while Approach 2 used wetland manager knowledge. Approach 2 predicted outflow and salinity better than Approach 1, and an important benefit was the simulation of water reuse within the wetland complex, which was previously not implemented. Approach 1 is generally suited for estimating pond depth when a model compartment represents one wetland, while Approach 2 is suited for wetlands with large spatial extent, many hydrological features, and managed flows. The improved model will support wetland management.

Policy Innovation and Governance for Irrigation Sustainability in the Arid, Saline San Joaquin River Basin

This paper provides a chronology and overview of events and policy initiatives aimed at addressing irrigation sustainability issues in the San Joaquin River Basin (SJRB) of California. Although the SJRB was selected in this case study, many of the same resource management issues are being played out in arid, agricultural regions around the world. The first part of this paper provides an introduction to some of the early issues impacting the expansion of irrigated agriculture primarily on the west side of the San Joaquin Valley and the policy and capital investments that were used to address salinity impairments to the use of the San Joaquin River (SJR) as an irrigation water supply. Irrigated agriculture requires large quantities of water if it is to be sustained, as well as supply water of adequate quality for the crop being grown. The second part of the paper addresses these supply issues and a period of excessive groundwater pumping that resulted in widespread land subsidence. A joint federal and state policy response that resulted in the facilities to import Delta water provided a remedy that lasted almost 50 years until the Sustainable Groundwater Management Act of 2014 was passed in the legislature to address a recurrence of the same issue. The paper describes the current state of basin-scale simulation modeling that many areas, including California, are using to craft a future sustainable groundwater resource management policy. The third section of the paper deals with unique water quality issues that arose in connection with the selenium crisis at Kesterson Reservoir and the significant threats to irrigation sustainability on the west side of the San Joaquin Valley that followed. The eventual policy response to this crisis was incremental, spanning two decades of University of California-led research programs focused on finding permanent solutions to the salt and selenium contamination problems constraining irrigated agriculture, primarily on the west side. Arid-zone agricultural drainage-induced water quality problems are becoming more ubiquitous worldwide. One policy approach that found traction in California is an innovative variant on the traditional Total Maximum Daily Load (TMDL) approach to salinity regulation, which has features in common with a scheme in Australia’s Hunter River Basin. The paper describes the real-time salinity management (RTSM) concept, which is geared to improving coordination of west side agricultural and wetland exports of salt load with east side tributary reservoir release flows to improve compliance with river salinity objectives. RTSM is a concept that requires access to continuous flow and electrical conductivity data from sensor networks located along the San Joaquin River and its major tributaries and a simulation model-based decision support designed to make salt load assimilative capacity forecasts. Web-based information dissemination and data sharing innovations are described with an emphasis on experience with stakeholder engagement and participation. The last decade has seen wide-scale, global deployment of similar technologies for enhancing irrigation agriculture productivity and protecting environmental resources.

Bringing statistical learning machines together for hydro-climatological predictions - Case study for Sacramento San joaquin River Basin, California

Study regionSacramento San Joaquin River Basin, California Study focusThe study forecasts the streamflow at a regional scale within SSJ river basin with largescale climate variables. The proposed approach eliminates the bias resulting from predefined indices at regional scale. The study was performed for eight unimpaired streamflow stations from 1962–2016. First, the Singular Valued Decomposition (SVD) teleconnections of the streamflow corresponding to 500 mbar geopotential height, sea surface temperature, 500 mbar specific humidity (SHUM500), and 500 mbar U-wind (U500) were obtained. Second, the skillful SVD teleconnections were screened non-parametrically. Finally, the screened teleconnections were used as the streamflow predictors in the non-linear regression models (K-nearest neighbor regression and data-driven support vector machine). New hydrological insightsThe SVD results identified new spatial regions that have not been included in existing predefined indices. The nonparametric model indicated the teleconnections of SHUM500 and U500 being better streamflow predictors compared to other climate variables. The regression models were capable to apprehend most of the sustained low flows, proving the model to be effective for drought-affected regions. It was also observed that the proposed approach showed better forecasting skills with preprocessed large scale climate variables rather than using the predefined indices. The proposed study is simple, yet robust in providing qualitative streamflow forecasts that may assist water managers in making policy-related decisions when planning and managing watersheds.

Relating survival of fall-run Chinook Salmon through the San Joaquin Delta to river flow

Survival of juvenile fall-run Chinook Salmon Oncorhynchus tshawytscha from the San Joaquin River (SJR) during their migration through the Sacramento-San Joaquin Delta of California has been low in recent years, and there is uncertainty about the role of river flow on survival. Five years (2010–2014) of acoustic telemetry data from juvenile hatchery-reared salmon offer spatially detailed survival information through this region. Multinomial regression and generalized linear models were used to relate survival to river flow in the SJR and its distributary, Old River (OR), on various spatial and temporal scales. Higher survival to Delta exit (rkm 77 from Golden Gate Bridge) was associated with higher root mean square of OR flow in the strongly tidal interior Delta (rkm 123; P < 0.0001), but not with higher SJR flow either entering the Delta from upstream (rkm 196; P = 0.2795) or measured in the Delta near the riverine/tidal interface (rkm 150; P = 0.3845). Survival in the upstream, more riverine region of the Delta was positively associated with SJR flow measured at rkm 150 and average net flow in the interior Delta (P ≤ 0.0001 for each), suggesting different mechanisms driving survival in the upstream versus downstream reaches of the Delta. The spatial complexity of the survival-flow relationship suggests that efforts to maximize total Delta survival should focus on a sequence of smaller regions, tailoring management strategies to each region rather than a single strategy for the Delta as a whole. Highly variable environmental conditions in this region combined with very low survival require more data to fully address the complex survival-flow relationship, both more years of data on various spatial scales and larger sample sizes of acoustic-tagged fish.

Excess N2 and denitrification in hyporheic porewaters and groundwaters of the San Joaquin River, California

The San Joaquin River (SJR) in California is purported to receive high nitrate loadings from surrounding agricultural lands through both surface and groundwater inputs. To investigate the potential removal of nitrate (NO3−) from surface and ground water sources, the spatial variations in dinitrogen (N2) gas concentrations and direct measurements of sediment denitrification potential (DNP), with amended NO3− and carbon (C) treatments, were investigated in the summer along a 95-km reach of the San Joaquin River. Excess N2 in hyporheic porewaters ranged from <0.1 to 8.65 mg L−1 and was significantly higher in porewaters from the 1.3 m (ground water source) versus 0.3 m (mixed surface and ground water) depths. In deep groundwater wells (3–7 m), median excess N2 concentration was 5.39 mg L−1 (range = <0.1–14.6 mg L−1). Excess N2 concentrations were inversely correlated with dissolved oxygen and NO3− concentrations suggesting denitrification as an important process in the dominantly anaerobic sediments. Hyporheic porewater NO3− concentrations exceeded the detection limit of 0.01 mg L−1 in only 20% of the hyporheic porewaters, in spite of high NO3− concentrations measured in both surface waters (mean = 2.25 mg N L−1) and surrounding groundwaters. Sediment DNP rates averaged 253 and 297 μg N kg−1 hr−1 for NO3− amended, and NO3− + C amended sediments, respectively, supporting the prevalence of denitrification in hyporheic sediments. Our results indicate that the hyporheic/riparian zones act as an anoxic barrier to nitrate transport from regional groundwater and as a location to remove NO3− from surface waters exchanging with the hyporheic zone.

Water Budgets for the Delta Watershed: Putting Together the Many Disparate Pieces

Water budgets integrate and summarize the water inputs and outputs that are essential for effective water resources management. Using water data collected from different sources, we constructed three water budgets (a 12-year annual average, a wet year, and a critically dry year) for the Sacramento–San Joaquin Delta (Delta), the Sacramento River (SR) watershed, and the San Joaquin River (SJR) watershed. Although multiple water budgets for the Delta exist, the water budgets presented here are the first to provide all three of the following: (1) water budgets for the entire Delta watershed, divided into management-relevant components, (2) comparisons between wet and dry years and between different regions of the watershed, and (3) discussion of major gaps and uncertainties in the available water data to guide and inform future data collection and water management. Results show that, from 1998 to 2009, the Delta received 24.2 million acre feet (maf) of water each year on average, which primarily exited the Delta as river outflow (71%), water exports (22%), and evapotranspiration (ET; 6%). The SR watershed received 56.9 maf of water (95% as precipitation). The major outputs from the SR watershed were ET (63%) and flows to the Delta (34%). In the SJR watershed, total water input was 28.7 maf composed of precipitation (74%), water imported from the Delta (18%), and storage depletion (7%). The major outputs from the SJR watershed were ET (65%), water exports (19%), and flows to the Delta (14%). Most values varied greatly from year to year. Although streamflows, water exports, and valley precipitation are relatively well measured and estimated, uncertainties are higher for groundwater storage change as well as for ET and precipitation in montane regions. Improvement in data collection and synthesis in these components is necessary to build a more detailed and accurate water budget.

Anadromous Salmonids in the Delta: New Science 2006-2016

As juvenile salmon enter the Sacramento–SanJoaquin River Delta (“the Delta”) they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited.Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use theDelta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

Evaluation of watershed-derived mass loads to prioritize TMDL decision-making.

A total maximum daily load (TMDL) for oxygen demanding substances is being implemented in the San Joaquin River (SJR) in California (USA) due to frequently occurring low dissolved oxygen conditions. The SJR is a eutrophic river, heavily impacted by agriculture. A mass balance was developed to identify the sources of oxygen-demanding substances and nutrients to the river with the objective of providing a scientific basis for management actions needed to meet TMDL requirements. Data were collected for flow and water quality and mass loads calculated for sites within the main stem of the SJR, river inputs (tributaries), and diversions in the study area. Using a quadrant analysis, tributary flows and loads are ranked to identify targets for water quality improvement efforts. Additionally, all mass loads were summed (inputs minus diversions) and compared with observed loads at the downstream limit of the study area. The mass balance analysis identifies major contributors of mass loads and mass balance closure is assessed for each constituent. These analysis methods inform the TMDL process which includes a load allocation, and is useful for determining locations for implementation of improvement projects needed to improve the health of the river.

Managing Water Resources Conflicts: Modelling Behavior in a Decision Tool

While technical tools for analysis of water resources systems have advanced, the major issue in resolving problems focuses on the interaction of human and natural systems. Agent-based modeling (ABM) has recently been used as an effective tool to develop integrated human-environmental models. One of the main challenges of ABM application in water resources management is to identify and characterize key agents. We provided recommendations to characterize agents normally involved in water decisions, and developed a framework for a conflict management tool, comprised of three models: a watershed simulation, an optimization, and a behavioral simulation model. The optimization-simulation model determined tradeoffs between the objective functions. The behavioral simulation model, developed based on ABM, simulated stakeholders interactions and their reactions to water allocation decisions. This model evaluated the applicability of different management scenarios to achieve specific rates of reduction in agricultural water allocations, selected from the tradeoffs. To develop and adjust this model, key stakeholders were identified in the San Joaquin River (SJR) watershed, California, and a survey was administered. The proposed recommendations and framework provides a new and innovative way to identify institutional interconnections, formulate and simulate their interactions, and create a hydrologic-environmental-human interface to support powerful decision-support tools to manage conflicts and make informed, practical decisions in water resources.

Delta Flow Factors Influencing Stray Rate of Escaping Adult San Joaquin River Fall-Run Chinook Salmon (Oncorhynchus tshawytscha)

Adult salmon that stray when they escape into non-natal streams to spawn is a natural phenomenon that promotes population growth and genetic diversity, but excessive stray rates impede adult abundance restoration efforts. Adult San Joaquin River (SJR) Basin fall-run Chinook salmon (Oncorhynchus tshawytscha) that return to freshwater to spawn migrate through the San Francisco Bay and Sacramento–San Joaquin River Delta (Delta). The Delta has been heavily affected by land development and water diversion. During the fall time-period for the years 1979 to 2007 Delta pumping facilities diverted on average 340% of the total inflow volume that entered the Delta from the SJR. The hypothesis tested in this paper is that river flow and Delta exports are not significantly correlated with SJR salmon stray rates. Adult coded-wire-tagged salmon recoveries from Central Valley rivers were used to estimate the percentage of SJR Basin salmon that strayed to the Sacramento River Basin. SJR salmon stray rates were negatively correlated (P = 0.05) with the average magnitude of pulse flows (e.g., 10 d) in mid- to late-October and positively correlated (P = 0.10) with mean Delta export rates. It was not possible to differentiate between the effects of pulse flows in October and mean flows in October and November on stray rates because of the co-linearity between these two variables. Whether SJR-reduced pulse flow or elevated exports causes increased stray rates is unclear. Statistically speaking the results indicate that flow is the primary factor. However empirical data indicates that little if any pulse flow leaves the Delta when south Delta exports are elevated, so exports in combination with pulse flows may explain the elevated stray rates. For management purposes, we developed two statistical models that predict SJR salmon stray rate: (1) flow and export as co-independent variables; and (2) south Delta Export (E) and SJR inflow (I) in the form of an E:I ratio.&nbsp;

Diel patterns of algae and water quality constituents in the San Joaquin River, California, USA

The San Joaquin River (SJR) is a hypereutrophic river that contributes to hypoxia in the downstream Stockton Deep Water Ship Channel. Oxidizable materials, in the form of algal biomass from upstream sources, contribute to the hypoxic conditions, especially from July to October. Our earlier work demonstrated the existence of strong chlorophyll- a diel cycles which complicated the calculation of algal loads for the watershed-scale monitoring program, necessary to address the total maximum daily load (TMDL) for dissolved oxygen (DO). The purpose of this study was to determine if diel patterns existed for other water quality constituents, and to determine the role of algal growth dynamics in driving these diel changes. Studies conducted between 30 June and 15 October 2004 evaluated temporal changes for several water quality constituents over four, 48 h studies at two sites along the mainstem of the SJR. Strong diel (24 h) patterns were observed for chlorophyll- a and pheophytin- a (algal pigments), temperature, DO, pH, dissolved inorganic nitrogen (DIN, NH 4 +-N + NO 3 −-N), soluble reactive phosphorus (SRP), and volatile suspended solids (VSS). Patterns of DIN and SRP were inverse of those observed for algal pigments, temperature, DO, pH, and VSS. The observed diel patterns of algal pigments and temperature were greater in the beginning of the summer (June/July) and diminished by the end of summer (September/October) due to the decreased photoperiod. Within a 24 h period the fluctuations observed in algal pigments and nutrients suggest that growth of algae during daylight hours and depletion at night are largely responsible for the observed diel patterns. Due to the observed diel variability in these water quality constituents, the samples collected for TMDL programs may not be representative unless samples are collected at the daily mean for a system.

Disinfection Byproduct Formation Potentials of Wetlands, Agricultural Drains, and Rivers and the Effect of Biodegradation on Trihalomethane Precursors

Trihalomethane (THM) precursors are a significant problem in the San Joaquin River (SJR) watershed, an important source of drinking water for >20 million people. Trihalomethane precursors diminish drinking water quality and are formed during natural decomposition of organic matter in aquatic systems. This study sought to identify sources of chlorine-reactive dissolved organic carbon (DOC) in the SJR watershed and to determine if wetlands were more important sources of THM precursors than nearby rivers and agricultural drains. The effects of biodegradation on DOC quality and quantity were investigated and analyzed across drainage type. Results show wetland drainage contained comparable bromide concentrations and organic carbon aromaticity but contained more than two times the average DOC concentrations found in agricultural drains and rivers. Wetland DOC did not have an increased propensity to form THMs when compared with the other drainage types, despite significantly higher wetland formation potentials. The higher formation potentials measured in wetland drainages were attributed to higher DOC concentrations; the positive correlation found between DOC and trihalomethane formation potentials (THMFPs) and the significantly higher wetland DOC concentrations suggest that increased wetland restoration could result in increased THMFPs in the SJR watershed. Wetland THM precursors were more resistant to biodegradation than THM precursors from agricultural and river samples. Results suggest that THM precursors in the SJR were from algae and were biodegraded.

Plant community, primary productivity, and environmental conditions following wetland re-establishment in the Sacramento-San Joaquin Delta, California

Wetland restoration can mitigate aerobic decomposition of subsided organic soils, as well as re-establish conditions favorable for carbon storage. Rates of carbon storage result from the balance of inputs and losses, both of which are affected by wetland hydrology. We followed the effect of water depth (25 and 55 cm) on the plant community, primary production, and changes in two re-established wetlands in the Sacramento San-Joaquin River Delta, California for 9 years after flooding to determine how relatively small differences in water depth affect carbon storage rates over time. To estimate annual carbon inputs, plant species cover, standing above- and below-ground plant biomass, and annual biomass turnover rates were measured, and allometric biomass models for Schoenoplectus (Scirpus) acutus and Typha spp., the emergent marsh dominants, were developed. As the wetlands developed, environmental factors, including water temperature, depth, and pH were measured. Emergent marsh vegetation colonized the shallow wetland more rapidly than the deeper wetland. This is important to potential carbon storage because emergent marsh vegetation is more productive, and less labile, than submerged and floating vegetation. Primary production of emergent marsh vegetation ranged from 1.3 to 3.2 kg of carbon per square meter annually; and, mid-season standing live biomass represented about half of the annual primary production. Changes in species composition occurred in both submerged and emergent plant communities as the wetlands matured. Water depth, temperature, and pH were lower in areas with emergent marsh vegetation compared to submerged vegetation, all of which, in turn, can affect carbon cycling and storage rates.

Investigation of river eutrophication as part of a low dissolved oxygen total maximum daily load implementation

In the United States, environmentally impaired rivers are subject to regulation under total maximum daily load (TMDL) regulations that specify watershed wide water quality standards. In California, the setting of TMDL standards is accompanied by the development of scientific and management plans directed at achieving specific water quality objectives. The San Joaquin River (SJR) in the Central Valley of California now has a TMDL for dissolved oxygen (DO). Low DO conditions in the SJR are caused in part by excessive phytoplankton growth (eutrophication) in the shallow, upstream portion of the river that create oxygen demand in the deeper estuary. This paper reports on scientific studies that were conducted to develop a mass balance on nutrients and phytoplankton in the SJR. A mass balance model was developed using WARMF, a model specifically designed for use in TMDL management applications. It was demonstrated that phytoplankton biomass accumulates rapidly in a 88 km reach where plankton from small, slow moving tributaries are diluted and combined with fresh nutrient inputs in faster moving water. The SJR-WARMF model was demonstrated to accurately predict phytoplankton growth in the SJR. Model results suggest that modest reductions in nutrients alone will not limit algal biomass accumulation, but that combined strategies of nutrient reduction and algal control in tributaries may have benefit. The SJR-WARMF model provides stakeholders a practical, scientific tool for setting remediation priorities on a watershed scale.

Changes in sediment and organic carbon accumulation in a highly-disturbed ecosystem: The Sacramento-San Joaquin River Delta (California, USA)

We used the Sacramento-San Joaquin River Delta CA (Delta, hereafter) as a model system for understanding how human activities influence the delivery of sediment and total organic carbon (TOC) over the past 50–60 years. Sediment cores were collected from sites within the Delta representing the Sacramento River (SAC), the San Joaquin River (SJR), and Franks Tract (FT), a flooded agricultural tract. A variety of anthropogenic tracers including 137Cs, total DDE (∑DDE) and brominated diphenyl ether (BDE) congeners were used to quantify sediment accumulation rates. This information was combined with total organic carbon (TOC) profiles to quantify rates of TOC accumulation. Across the three sites, sediment and TOC accumulation rates were four to eight-fold higher prior to 1972. Changes in sediment and TOC accumulation were coincident with completion of several large reservoirs and increased agriculture and urbanization in the Delta watershed. Radiocarbon content of TOC indicated that much of the carbon delivered to the Delta is “pre-aged” reflecting processing in the Delta watershed or during transport to the sites rather than an input of predominantly contemporary carbon (e.g., 900–1400 years BP in surface sediments and 2200 yrs BP and 3610 yrs BP at the base of the SJR and FT cores, respectively). Together, these data suggest that human activities have altered the amount and age of TOC accumulating in the Delta since the 1940s.

Environmental decision support system development for seasonal wetland salt management in a river basin subjected to water quality regulation

Seasonally managed wetlands in the Grasslands Basin on the west-side 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 wetlands contain salt which, when drained to the San Joaquin River (SJR) during the annual drawdown period, can negatively impact water quality and cause concern to downstream agricultural riparian water diverters. Recent environmental regulation, limiting discharges salinity to the SJR and primarily targeting agricultural non-point sources, now also targets return flows from seasonally managed wetlands. Real-time water quality management has been advocated as a means of continuously matching salt loads discharged from agricultural, wetland and municipal operations to the assimilative capacity of the SJR. Past attempts to build environmental monitoring and decision support systems (EDSS’s) to implement this concept have enjoyed limited success for reasons that are discussed in this paper. These reasons are discussed in the context of more general challenges facing the successful implementation of a comprehensive environmental monitoring, modelling and decision support system for the SJR Basin.

Ranking tributaries for setting remediation priorities in a TMDL context

The San Joaquin River (SJR) in the Central Valley of California has been designated an impaired waterbody based on its loss of fisheries-related beneficial uses and the river is now subject to regulation under total maximum daily load (TMDL) rules. For impaired waterbodies, numeric standards alone may not be sufficient to establish remediation priorities and priorities must be established by comparing drainages to each other. Data collected as part of regional water quality (WQ) studies in the SJR Valley were not normally distributed, so nonparametric methods based on ranking were used to compare the WQ of individual tributaries and drainages. Normalized rank means (NRMs) were calculated from ranked data and NRMs were mapped to identify priority drainages for WQ improvement activities. NRMs for individual parameters were combined into indexes that are useful for examining the relative importance of different drainages for multiple parameters simultaneously. Indexes were developed for eutrophication and overall WQ. This ranking approach is being proposed as an easily understood, transparent, and scientifically rigorous method to assess the relative WQ impact of individual drainages and set watershed remediation priorities.

Comparison of wetland and agriculture drainage as sources of biochemical oxygen demand to the San Joaquin River, California

For many years, the San Joaquin River (SJR) has had low dissolved oxygen conditions intermittently during the late summer and early fall. The low dissolved oxygen conditions are impacting critical fish habitat and the SJR is being regulated under a state of California remediation plan that includes the development of a total maximum daily load (TMDL) allocation for oxygen demanding substances. In support of the development of a scientific TMDL allocation, studies are being conducted to characterize water quality in the many tributaries of the SJR. This study identified the sources of biochemical oxygen demand (BOD) in two western tributaries of the SJR, Mud Slough and Salt Slough, and measured the loads of BOD, algae, and ammonia entering the SJR from wetland and agricultural sources. Mud and Salt Sloughs drain the Grassland Watershed. The watershed contains seasonal wetlands, irrigated farmland, and other agricultural lands. This drainage is under close regulatory scrutiny, because it produces a majority of the selenium and boron entering the SJR. In this study, wetland and irrigated agricultural drainage were sampled separately and a comparison was made to determine differences in water quality. In addition, water entering the study area was compared to water exiting the study area to determine the effect of water use in the region on water quality. This study demonstrated that BOD loads from the Grassland Watershed to the SJR were proportional to flow during June–October, the most critical time for dissolved oxygen deficits in the lower SJR. This indicates that Mud and Salt Sloughs are not producing more BOD than other tributaries in the region that are not under close regulatory scrutiny. The BOD concentration of wetland drainage is higher than that of agricultural drainage, but the higher agricultural drainage flows result in a higher mass loading of BOD. Wetland flooding and irrigation of crops both had a negative impact on water quality. Algal growth was identified as the major source of BOD in agricultural drainage and locations where BOD control could potentially be implemented were identified.

Biological Oxygen Demand Dynamics in the Lower San Joaquin River, California

Dissolved oxygen less than 5 mg L(-1) (U. S. EPA advisory level) commonly occurs in the lower San Joaquin River (SJR), California. Most acute episodes typically occur in late summer and fall. The oxygen deficit can stress and kill aquatic organisms, often inhibiting the upstream migration of Chinook salmon (Oncorhynchus tshawytscha). This 5 year study examined watershed-scale spatial and temporal biological oxygen demand (BOD) loads and the primary components believed to contribute to BOD: ammonium, algal biomass, nonalgal particulate organic carbon, dissolved organic carbon, and dissolved organic nitrogen. Samples were collected bimonthly at 15 sites during the summers of 2000 and 2001 and from three lower mainstem sites from May 2002 to March 2005. BOD loads showed a downstream increase in parallel with increasing algal biomass loads resulting primarily from in-stream growth. BOD loads from measured tributaries and drains accounted for 28% and 39% of the BOD load at the downstream Vernalis site in 2000 and 2001, respectively. Algal C was positively correlated (r=0.80) with BOD, explaining 64% of BOD variance for data collected from 2001 to 2005. Less than 20% of BOD was found in the dissolved fraction (<0.45 microm). We conclude that algal biomass is the primary contributor to BOD loads in the lower SJR, upstream of Mossdale.