Dispersion and Stratification Dynamics in the Upper Sacramento River Deep Water Ship Channel

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosystems through their influence on primary production. The San Francisco Estuary (estuary) is a low-productivity ecosystem, which is in part responsible for constraining higher trophic levels, including fishes. Many research and habitat-restoration efforts trying to increase primary production have been conducted, including, as described here, a whole-ecosystem nutrient addition experiment where calcium nitrate was applied in the Sacramento River Deep Water Ship Channel (DWSC) to see if phytoplankton production could be increased and exported out of the DWSC. As an integral part of this experiment, we investigated the physical mechanisms that control mixing, and how these mechanisms affect the strength and duration of thermal stratification, which we revealed as critical for controlling phytoplankton dynamics in the relatively turbid upper DWSC. Analysis of a suite of mixing mechanisms and time-scales show that both tidal currents and wind control mixing rates and stratification dynamics in the DWSC. Longitudinal and vertical dispersion increased during periods of high wind, during which wind speed influenced dispersion more than tidal currents. Thermal stratification developed most days, which slowed vertical mixing but was rapidly broken down by wind-induced mixing. Stratification rarely persisted for longer than 24 hours, limiting phytoplankton production in the study area. The interaction between physical mechanisms that control mixing rates, mediate stratification dynamics, and ultimately limit primary production in the DWSC may be useful in informing habitat restoration elsewhere in the Delta and in other turbid aquatic environments.

Patterns of Water Use in California

Recent patterns of water use and supply in California are presented based on a new data set compiled from the California Department of Water Resources water balance data for 2002 through 2016. The water use and supply include surface water and groundwater, although groundwater reporting has been incomplete. These data are used to support the Water Plan released every 3 to 5 years and are the most comprehensive and finest spatial- and temporal-scale data set for California water resources. First, using the Bay–Delta watershed as a case example, we show that recent fluctuations in water use are highly correlated with variations in precipitation. Developed water supplies and use show these fluctuations, but they are modified by reservoir inflows and releases, groundwater supplies, and Delta outflows. Second, although the annually precipitated water supply in the Bay–Delta varies by about 30%, the developed water supply damps this considerably. The water management system maintained nearly constant agricultural water use even in periods of intense drought, with year-to-year variation of about 7%. Variability in urban water use is higher (∼20%), largely from conservation during periods of drought. Finally, this information can help improve water resource management because it connects regional-scale data to meaningful policy decision-making at county and sub-county levels. At a time when water policy and management are being re-evaluated across the American West in the light of changing climate, decision-making informed by science and data is urgently needed. The statewide water balance data provide the means to establish a consistent, quantitative framework for water resource analysis throughout the state.

A Survey of X2 Isohaline Empirical Models for the San Francisco Estuary

This work surveys the performance of several empirical models, all recalibrated to a common data set, that were developed over the past 25 years to relate freshwater flow and salinity in the San Francisco Estuary (estuary). The estuary’s salinity regime—broadly regulated to meet urban, agricultural, and ecosystem beneficial uses—is managed in spring and certain fall months to meet ecosystem objectives by controlling the 2 parts per thousand bottom salinity isohaline position (referred to as X2). We tested five empirical models for accuracy, mean, and transient behavior. We included a sixth model, employing a machine learning framework and variables other than outflow, in this survey to compare fitting skill, but did not subject it to the full suite of tests applied to the other five empirical models. Model performance was observed to vary with hydrology, year, and season, and in some cases exhibited unique limitations as a result of mathematical formulation. However, no single model formulation was found to be consistently superior across a wide range of tests and applications. One test revealed that the models performed equally well when recalibrated to a uniformly perturbed input time-series. Thus, while the models may be used to identify anomalies or seasonal biases (the latter being the subject of a companion paper), their use as inverse models to infer freshwater outflow to the estuary from salinity observations is not expected to improve upon the absolute accuracy of existing outflow estimates. This survey suggests that, for analyses that span a long hydrologic record, an ensemble approach—rather than the use of any individual model on its own—may be preferable to exploit the strengths of individual models.

Apparent Seasonal Bias in Delta Outflow Estimates as Revealed in the Historical Salinity Record of the San Francisco Estuary: Implications for Delta Net Channel Depletion Estimates

Accurate estimates of freshwater flow to the San Francisco Estuary are important in successfully regulating this water body, in protecting its beneficial uses, and in accurately modeling its hydrodynamic and water-quality transport regime. For regulatory purposes, freshwater flow to the estuary is not directly measured; rather, it is estimated from a daily balance of upstream Delta inflows, exports, and in-Delta water use termed the net Delta outflow index (NDOI). Field research in the 1960s indicated that NDOI estimates are biased low in summer–fall and biased high in winter–spring as a result of conflating Delta island evapotranspiration estimates with the sum of ungauged hydrologic interactions between channels and islands referred to as net channel depletions. In this work, we employed a 50-year observed salinity record along with gauged tidal flows and an ensemble of five empirical flow-salinity (X2) models to test whether a seasonal bias in Delta outflow estimates could be inferred. We accomplished this objective by conducting statistical analyses and evaluating whether model skill could be improved through seasonal NDOI flow adjustments. Assuming that model residuals are associated with channel depletion uncertainty, our findings corroborate the 1960s research and suggest that channel depletions are biased low in winter months (i.e., NDOI is biased high) and biased high in late summer and early fall months (i.e., NDOI is biased low). The magnitude of seasonal bias, which can reach 1,000 cfs, is a small percentage of typical winter outflow but represents a significant percentage of typical summer outflow. Our findings were derived from five independently developed models, and are consistent with the physical understanding of water exchanges on the islands. This work provides motivation for improved characterization of these exchanges to improve Delta outflow estimates, particularly during drought periods when water supplies are scarce and must be carefully managed.

Concentrations, Loads, and Associated Trends of Nutrients Entering the Sacramento–San Joaquin Delta, California

Statistical modeling of water-quality data collected at the Sacramento River at Freeport and San Joaquin River near Vernalis, California, USA, was used to examine trends in concentrations and loads of various forms of dissolved and particulate nitrogen and phosphorus that entered the Sacramento–San Joaquin River Delta (Delta) from upstream sources between 1970 and 2019. Ammonium concentrations and loads decreased at the Sacramento River site from the mid-1970s through 1990 because of the consolidation of wastewater treatment and continuously reduced from the mid-1970s to 2019 at the San Joaquin River site. Current ammonium concentrations are mostly below 4 µM (0.056 mg N L–1) at both sites, a concentration above which reductions in phytoplankton productivity or changes in algal species composition may occur. The Sacramento River at Freeport site is located upstream of the Sacramento Regional County Sanitation District’s treatment facility’s discharge point; nutrient water quality there is representative of upstream sources. Inorganic nitrogen (nitrate plus ammonium) concentrations and loading differed at both sites. At the Sacramento River location, concentrations decrease in the summer agricultural season, reducing the molar ratios of nitrogen to phosphorus. In contrast, inorganic nitrogen concentrations increase in the San Joaquin River during the agricultural season as a result of irrigation runoff, increasing the molar ratio of nitrogen to phosphorus. This increase suggests a possible nitrogen limitation in the northern Delta and a phosphorus limitation in the southern Delta, as indicated by the molar ratios of bioavailable nitrogen to bioavailable phosphorus. Planned upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) will reduce inorganic nitrogen inputs to the northern Delta. Consequently, the supply of bioavailable nitrogen throughout the upper estuary should diminish. Source modeling of nitrogen and phosphorus identifies agriculture, atmospheric deposition, and wastewater effluent as sources of total nitrogen in the Central Valley. In contrast, geologic sources, agriculture, and wastewater discharge are the primary sources of phosphorus.

Wetland Availability and Salinity Concentrations for Breeding Waterfowl in Suisun Marsh, California

Availability of wetlands with low salinities during the breeding season can influence waterfowl reproductive success and population recruitment. Salinities as low as 2 ppt (3.6 mScm–1) can impair duckling growth and influence behavior, with mortality occurring above 9 ppt (14.8 mScm–1). We used satellite imagery to quantify the amount of available water, and sampled surface water salinity at Grizzly Island, in the brackish Suisun Marsh, at three time-periods during waterfowl breeding (April, May, July) over 4 years (2016–2019). More water was available and salinity was lower during wetter years (2017, 2019) than during drier years (2016, 2018), and the amount of water in wetlands decreased 73%–86% from April to July. Across all time-periods and years, the majority (64%–100%) of wetland habitat area had salinities above what has been shown to negatively affect ducklings (> 2 ppt), and up to 42% of wetland area had salinities associated with duckling mortality (> 9 ppt). During peak duckling production in May, 81%–95% of available water had salinity above 2 ppt, and 5%–21% was above 9 ppt. In May of the driest year (2016), only 0.5 km2 of low-salinity water (< 2 ppt) was available to ducklings in the study area, compared to 2.6 km2 in May of the wettest year (2017). Private duck clubs own the majority of wetland habitat at Grizzly Island and consistently had a greater percentage of land flooded during summer than did publicly owned wetlands, but private wetlands generally had higher salinities than public wetlands, likely because they draw from higher-salinity water sources. By July, few wetlands remained flooded, and most had salinities high enough to impair duckling growth and survival. Local waterfowl populations would benefit from management practices that provide fresher water during peak duckling production in May and retain more water through July.

Simulated Fishing to Untangle Catchability and Availability in Fish Abundance Monitoring

In fisheries monitoring, catch is assumed to be a product of fishing intensity, catchability, and availability, where availability is defined as the number or biomass of fish present and catchability refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Programs often deal with this problem by assuming that catchability is constant, but if catchability is not constant, it is not possible to separate the effects of catchability and population size using monitoring data alone. This study uses individual-based simulation to separate the effects of changing environmental conditions on catchability and availability in environmental monitoring data. The simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies. Results of this study indicate that given constraints on Delta Smelt swimming ability, it is unlikely that the apparent declines in Delta Smelt abundance are the result of changing water clarity affecting catchability.

Use of a Managed Flow Pulse as Food Web Support for Estuarine Habitat

While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. As a test of this concept, in summer 2016, we used a managed flow pulse to target an ecologically important region: a freshwater tidal slough complex (Cache Slough Complex–CSC). Our goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt Hypomesus transpacificus. We used regional water infrastructure to direct 18.5 million m³ of Sacramento River flow into its adjacent Yolo Bypass floodplain, where the pulse continued through CSC. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between CSC and further downstream. Multiple water quality constituents (specific conductivity, dissolved oxygen, nutrients [NO₃ + NO₂, NH₄, PO₄]) varied across the study region, and showed a strong response to the flow pulse. In addition, the lower Sacramento River had increased phytoplankton biomass and improved food quality indices (estimated from long-chain essential fatty acids) after the flow pulse. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. This study was conducted during a single year, which may have had unique characteristics; however, we believe that our study is an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.

Food for Thought: Connecting Zooplankton Science to Management in the San Francisco Estuary

[Abstracts are not associated with Essays. - the SFEWS Editors]