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This work presents a simplified approach for estimating ionic concentrations from specific electrical conductance (EC) data in the San Francisco Estuary. Monitoring the EC of water through electrodes is simple and inexpensive. As a result, a wealth of high-resolution time-series data is available to indirectly estimate salinity concentrations and, by extension, seawater intrusion throughout the study domain. However, scientists and managers are also interested in quantifying ionic (e.g., bromide, chloride) and total dissolved solids (TDS) concentrations to meet water-quality regulations, protect beneficial uses, support environmental analyses, and track source-water dominance. These constituent concentrations, reported with lower spatial and temporal resolution than EC, are typically measured in the laboratory from discrete (grab) water samples. We divided the study domain into four unique regions to estimate concentrations of major ions and TDS as mathematical functions of measured or model-simulated EC. Salinity relationships in three of the four regions-- regions that represent Sacramento-San Joaquin Delta (Delta) inflow and seawater-dominated boundaries--reflect ionic make-ups that are either independent of or weakly dependent on season and hydrologic condition, and are highly correlated with EC. The fourth region--represented by the interior Delta--exhibits salinity characteristics associated with complex-boundary source-water mixing that varies by season and hydrologic condition. We introduce a novel method to estimate ionic and dissolved solids concentrations within this fourth region, given month, water year type, and (optionally) X2 isohaline position, which allows for more accurate EC-based estimates than previously available. The resulting approach, while not a substitute for hydrodynamic modeling, can provide useful information under constrained schedules and budgets. [ABSTRACT FROM AUTHOR]

This paper presents a novel approach to estimate major ion concentrations in estuaries from a known specific conductance. Assuming two-source conservative mixing at steady state, we propose an extension of the Practical Salinity Scale 1978 to estimate concentrations of major ions and total dissolved solids as functions of the conductivity ratio, which is the ratio of sample conductivity and seawater conductivity. We employ an extensive salinity data set that includes measurements of specific conductance and concentrations of major ions and total dissolved solids to demonstrate its validity and limitations for the San Francisco estuary. We show the proposed extension to be valid in waters influenced by seawater intrusion at specific conductance values greater than or equal to 0.25 mS/cm and propose adjusted model constants to account for ionic composition under less saline conditions. We observed evidence of seasonal bias in model residuals and hypothesize that this bias is related to the simplified assumption of fixed upstream end member concentrations. This finding of seasonal bias suggests that upstream end member concentrations are more reflective of high alkalinity freshwater contributions from December through June, compared to other months. [ABSTRACT FROM AUTHOR]

The deviation of specific electrical conductance (EC) from conservative mixing behavior is well-established in the scientific literature. This principle is based on the observation that, as salt concentration in a water sample increases, the mobility of individual ions in the sample decreases, and thus their ability to conduct electricity decreases. Despite this fact, some commonly used models for salinity transport in the San Francisco Estuary (estuary) utilize EC as a primary simulation constituent, treating it as a conservative quantity. Such a modeling approach has likely been followed to exploit the wide availability of EC data for model calibration and validation, and to obviate the need to translate between EC and salinity in a domain characterized by multiple source waters with varying ionic make-ups. Arguably, this approach provides a reasonable tradeoff between data translation error and model simulation error. In this paper, we critically evaluate this approach, employing an extensive salinity data set that includes measurements of EC and major ion concentrations in the estuary. We demonstrate and quantify EC deviation from steady-state, conservative mixing behavior; review the conservative mixing behavior of three bulk salinity measures (practical salinity, ionic strength, and limiting equivalent conductance); and evaluate their source-dependent correlations with EC in the estuary. We find limiting equivalent conductance--a value that assumes uninhibited mobility among individual ions in a water sample--to be an attractive alternative for salinity transport in the estuary. In addition to being a conservative quantity, it is consistently correlated with EC in the estuary's dominant source waters, and thus addresses concerns related to data-translation error. We conclude this paper discussing pros and cons of adopting various salinity-transport model constituents. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We evaluated two historically important data sets to characterize the San Francisco Estuary's salinity regime before the State of California began systematic data collection in the early 1920s. One set documents barge travel along the Sacramento and San Joaquin rivers to obtain water of adequate quality for local industry; a second set documents Delta inflow used to compute antecedent outflow. The barge travel distance reported over 2 decades (1908-1929) was well explained by flow-salinity modeling, indicating internal consistency in these measurements. However, absolute salinity intrusion estimated through the barge travel data is systematically lower than suggested by contemporaneous water-quality measurements available since 1921. Through integration of these data sets, our work showed substantial similarities between 1908-1921 and the subsequent period before construction of Shasta Dam (1922-1944). Our analysis reveals an apparent shift in the estuary's salinity regime, with lesser salinity intrusion occurring in pre-1919 summer and fall months as a result of higher summer Delta outflow; this shift may be related to lower storage and irrigation diversions as well as a preponderance of wet years with higher summer runoff in the pre-1919 period. We found seasonal patterns of wet year salinity intrusion to be comparable over the full study period (1908-1944), indicating that the relative effect of upstream water management is minimal when flows are high, consistent with findings reported in later periods. The barge and flow data provide qualitative insights on early 20th century conditions, when limited data are available. Post-1920 hydrology and salinity data are preferable for quantitative analyses because of better documentation associated with collection and analysis, and sustained reporting over several decades. This work provides a foundation for future efforts to characterize the hydrologic and hydrodynamic changes that occurred in the system between the 1850s (i.e., natural or pre-development conditions) and the 1920s. [ABSTRACT FROM AUTHOR]

The Practical Salinity Scale 1978 (PSS-78)—developed using samples of standard seawater—is widely used as a conductivity-based measure of salinity in oceans and estuaries. Here we evaluate the application of the scale across San Francisco Estuary where salinity reflects a mixture of seawater, riverine inflows, and agricultural return flows from islands within the estuary. We employ an extensive salinity data set that includes measurements of specific electrical conductance (EC) and major ion concentrations to demonstrate the scale's applicability in this estuary. We find the scale to be valid in waters dominated by seawater intrusion as well as in waters dominated by the largest riverine input to the estuary, i.e. the Sacramento River. In these waters, we further find that the scale to be valid well below its recommended lower-bound value of 2.0. However, the scale under-estimates salinity in waters dominated by the San Joaquin River, the second largest riverine input to the estuary. Similarly, the scale under-estimates salinity in agricultural return flows to the estuary. This work shows that a singular PSS-78 relationship cannot be used to accurately compute salinity across the entire estuary from EC measurements—a finding of considerable importance for salinity monitoring and modeling applications. Using data from the estuary, we propose appropriate corrections to the scale for these drainage-influenced waters. We recommend further research into how these modified PSS-78 formulations can be used to more accurately estimate salinity and ionic constituent concentrations in this and other estuaries. [Display omitted] • Practical Salinity Scale 1978 (PSS-78) evaluated across San Francisco Estuary. • PSS-78 found to be valid in seawater dominated portions of estuary and in the major freshwater inflow (Sacramento River) well below the literature-recommended lower bound of 2.0. • PSS-78 found to underpredict salinity in the second major inflow and in agricultural drainage in the estuary. • PSS-78 does not appear to be accurate for estuary-wide salinity estimation. [ABSTRACT FROM AUTHOR]

This work presents updated reconstructions of watershed runoff to San Francisco Estuary from tree-ring data to AD 903, coupled with models relating runoff to freshwater flow to the estuary and salinity intrusion. We characterize pre-development freshwater flow and salinity conditions in the estuary over the past millennium and compare this characterization with contemporary conditions to better understand the magnitude and seasonality of changes over this time. This work shows that the instrumented flow record spans the range of runoff patterns over the past millennium (averaged over 5, 10, 20 and 100 years), and thus serves as a reasonable basis for planning-level evaluations of historical hydrologic conditions in the estuary. Over annual timescales we show that, although median freshwater flow to the estuary has not changed significantly, it has been more variable over the past century compared to pre-development flow conditions. We further show that the contemporary period is generally associated with greater spring salinity intrusion and lesser summer–fall salinity intrusion relative to the pre-development period. Thus, salinity intrusion in summer and fall months was a common occurrence under pre-development conditions and has been moderated in the contemporary period due to the operations of upstream reservoirs, which were designed to hold winter and spring runoff for release in summer and fall. This work also confirms a dramatic decadal-scale hydrologic shift in the watershed from very wet to very dry conditions during the late 19th and early 20th centuries; while not unprecedented, these shifts have been seen only a few times in the past millennium. This shift resulted in an increase in salinity intrusion in the first three decades of the 20th century, as documented through early records. Population growth and extensive watershed modification during this period exacerbated this underlying hydrologic shift. Putting this shift in the context of other anthropogenic drivers is important in understanding the historical response of the estuary and in setting salinity targets for estuarine restoration. By characterizing the long-term behavior of San Francisco Estuary, this work supports decision-making in the State of California related to flow and salinity management for restoration of the estuarine ecosystem. [ABSTRACT FROM AUTHOR]