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.

Trachyandesite of Kennedy Table, its vent complex, and post−9.3 Ma uplift of the central Sierra Nevada: Comment

Hildreth et al. (2021) analyzed a set of table mountains near the San Joaquin River that are capped by a 9.3 Ma trachyandesite lava flow and concluded that, since the deposition of the volcanic rocks, the table mountains have been tilted 1.07° due to uplift of the central Sierra Nevada. While Gabet (2014) suggested that, under a limited set of conditions, the size of fluvial gravels under the table mountains would support the hypothesis of postdepositional uplift, the authors claimed that their evidence is more definitive. In addition, the authors proposed that the central Sierra Nevada tilted as a rigid block. However, their analyses rely on inferences and assumptions that are not supported by field evidence.

Trachyandesite of Kennedy Table, its vent complex, and post−9.3 Ma uplift of the central Sierra Nevada: Reply

We thank Emmanuel Gabet for his interest in our work on the Trachyandesite of Kennedy Table and for the opportunity to more fully explain our methods. We (Hildreth et al., 2021) claimed that various lines of evidence from the lava flow strongly support ∼1° of tilting of the central Sierra Nevada since 9.3 Ma. Gabet (2021) stated, “However, their analyses rely on inferences and assumptions that are not supported by field evidence.” First, he addressed the issue of whether the sinuous lava-flow remnants east of Millerton Lake are fortuitously shaped erosional remnants of a planar lava flow, or whether they are fossilized meanders of the paleo−San Joaquin River, which he terms to be our “interpretation.” We strongly disagree with this characterization. In Hildreth et al. (2021), we treated the meander question as a hypothesis to be tested using topographic data.

Comparison of Deterministic and Statistical Models for Water Quality Compliance Forecasting in the San Joaquin River Basin, California

Model selection for water quality forecasting depends on many factors including analyst expertise and cost, stakeholder involvement and expected performance. Water quality forecasting in arid river basins is especially challenging given the importance of protecting beneficial uses in these environments and the livelihood of agricultural communities. In the agriculture-dominated San Joaquin River Basin of California, real-time salinity management (RTSM) is a state-sanctioned program that helps to maximize allowable salt export while protecting existing basin beneficial uses of water supply. The RTSM strategy supplants the federal total maximum daily load (TMDL) approach that could impose fines associated with exceedances of monthly and annual salt load allocations of up to $1 million per year based on average year hydrology and salt load export limits. The essential components of the current program include the establishment of telemetered sensor networks, a web-based information system for sharing data, a basin-scale salt load assimilative capacity forecasting model and institutional entities tasked with performing weekly forecasts of river salt assimilative capacity and scheduling west-side drainage export of salt loads. Web-based information portals have been developed to share model input data and salt assimilative capacity forecasts together with increasing stakeholder awareness and involvement in water quality resource management activities in the river basin. Two modeling approaches have been developed simultaneously. The first relies on a statistical analysis of the relationship between flow and salt concentration at three compliance monitoring sites and the use of these regression relationships for forecasting. The second salt load forecasting approach is a customized application of the Watershed Analysis Risk Management Framework (WARMF), a watershed water quality simulation model that has been configured to estimate daily river salt assimilative capacity and to provide decision support for real-time salinity management at the watershed level. Analysis of the results from both model-based forecasting approaches over a period of five years shows that the regression-based forecasting model, run daily Monday to Friday each week, provided marginally better performance. However, the regression-based forecasting model assumes the same general relationship between flow and salinity which breaks down during extreme weather events such as droughts when water allocation cutbacks among stakeholders are not evenly distributed across the basin. A recent test case shows the utility of both models in dealing with an exceedance event at one compliance monitoring site recently introduced in 2020.

Comparison of Length-at-Date Criteria and Genetic Run Assignments for Juvenile Chinook Salmon Caught at Sacramento and Chipps Island in the Sacramento–San Joaquin Delta of California

There are four distinct runs of Chinook Salmon (Oncorhynchus tshawytscha) in the Central Valley, named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, we use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit). Fin tissues were collected from approximately 7,500 juvenile Chinook Salmon captured in trawl samples between 2007 and 2011. Tissues were analyzed using 21 microsatellites to determine genetic run assignments for individuals, which we compared with LDC run assignments. Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.

Survival of a threatened salmon is linked to spatial variability in river conditions

Extirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-α, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

Trachyandesite of Kennedy Table, its vent complex, and post−9.3 Ma uplift of the central Sierra Nevada

Tectonic interpretation of the central Sierra Nevada—whether the crest of the Sierra Nevada (California, USA) was uplifted in the late Cenozoic or whether the range has undergone continuous down-wearing since the Late Cretaceous—is controversial, since there is no obvious tectonic explanation for renewed uplift. The strongest direct evidence for late Cenozoic uplift of the central Sierra Nevada comes from study of the Trachyandesite of Kennedy Table, which followed the course of the Miocene San Joaquin River but has a steeper gradient than the modern river. Early workers attributed this steeper gradient to tilting of the Sierra Nevada block since the late Miocene, resulting in 2 km of range-crest uplift. However, this interpretation has been contested on grounds that the Miocene river gradient had to be assumed and that the Sierran Batholith could have warped during tilting, thus failing to uplift the range crest. The objective of this study was to obtain quantitative data that test these criticisms. The Trachyandesite of Kennedy Table is a chain of 33 remnants of a single lava flow as thick as 65 m, preserved for 21 km from Squaw Leap to Little Dry Creek, close to the modern San Joaquin River in the foothills of the Sierra Nevada. Several remnants lie on fluvial gravel of the late Miocene San Joaquin River. Early workers speculated that the lava concealed its own (unrecognized) vent, but in 2011, we identified the vent on the Middle Fork of the San Joaquin River, 13.5 km south of Deadman Pass and 70 km northeast of Kennedy Table. The vent complex intrudes Cretaceous granite, has 285 m relief, and is an intricately jointed intrusion that grades up into a glassy lava flow. Composition (58% SiO2) and 40Ar/39Ar age (9.3 Ma) are identical at the vent and downstream. Basal elevations of remnants were recorded, and the present-day basal gradients of several were adjusted for apparent dip and projected along a vertical plane at 220° (the estimated tilt azimuth). The basal gradients are far steeper than that of the modern river, but they differ slightly from reach to reach and are thus inconsistent measures of the post-Miocene tilt. Likewise, relief eroded atop most remnants renders modeling of upper surfaces suspect. At Little Dry Creek, however, a chain of nine remnants rests on fluvial floodplain sand and gravel; this chain trends 230°, and its smooth basal contact now dips 1.36° (adjusted at 220°). Projection of this dip 89 km from the 207 m base of the most distal remnant at Little Dry Creek to the vent intrusion falls far below the 2760 m intrusion-to-lava-flow transition near the Sierran crest, showing that the Sierran block has not undergone pronounced convex warping. Using elevation data on paleoriver meanders preserved by the lava flow, we show that the paleogradient has a cosine dependence on meander-section azimuth, indicating tilting. Subtraction of 1.07° of dip restores the data to an azimuth-independent configuration, indicating total tilting since 9.3 Ma of 1.07° and an original large-scale gradient of 0.46°, similar to the published value of 0.33° at Squaw Leap, but larger than the previously obtained value of 0.057° at Little Dry Creek. Subtraction of those Miocene estimates from the observable 1.643° tilt along the section from Little Dry Creek to the vent yields vent uplift of 2464 m (for 0.057°), 1835 m (for 0.46°), and 2040 m (for 0.33°). Confirmation of earlier assumptions regarding Miocene river gradient and block rigidity greatly strengthens the case for ∼2 km of late Cenozoic uplift of the central Sierra Nevada crest.

Outmigration Survival of a Threatened Steelhead Population through a Tidal Estuary

Juvenile steelhead are exposed to numerous threats in heterogeneous, estuarine environments, yet understanding of survival patterns and processes during this migratory stage is often limited by studies that use surrogate species or are restricted in duration and spatial specificity. Lack of detailed survival information in this critical migratory stage limits the effectiveness of management to maintain juvenile life history diversity in threatened populations. We used acoustic telemetry with multistate release-recapture models to investigate survival patterns during a key stage of the juvenile emigration of anadromous steelhead through the Sacramento-San Joaquin River Delta of California, United States, over multiple years, including three drought years. Survival was highly variable both within and among the six years of the study; estimated total survival through the Delta ranged from 0.06 (May 2014) to 0.69 (March 2011). Survival in the upstream reaches was associated with river discharge into the Delta, while survival through the lower reaches was associated with migration route. The lack of a single factor associated with survival in all reaches counteracts preconceived ideas of survival processes. Hydrodynamic manipulation and habitat improvements are recommended to support this anadromous population in a changing climate.

Statistical Evaluation of Behavior and Population Dynamics Models Predicting Movement and Proportional Entrainment Loss of Adult Delta Smelt in the Sacramento–San Joaquin River Delta

There has been considerable debate about effects of entrainment of endangered Delta Smelt (Hypomesus transpacificus) at water export facilities located in the Sacramento–San Joaquin River Delta. In this paper we use a behavior-driven movement model (BMM) to simulate the movement of adult Delta Smelt, which, in conjunction with a population dynamics model, estimates the proportion of the population that is lost to entrainment, i.e., proportional entrainment loss (PEL). Parameters of the population model are estimated by maximum likelihood by comparing predictions to data from Fall Midwater Trawl (FMWT) and Spring Kodiak Trawl (SKT) surveys, as well as to daily salvage estimates. Our objectives are to evaluate different movement behavior hypotheses, to rank estimates of PEL based on how well predictions fit the data, and to sharpen our understanding of the data to inform future research and monitoring decisions. We applied the modeling framework to data from water year 2002—a year when salvage was high—and tested 30 combinations of six behavior and five population dynamics models. More complex process and observation assumptions in the population model led to much improved fits in most cases, but did not appreciably influence PEL predictions, which were largely determined by movement predictions from the BMMs. Estimates of PEL varied considerably among behaviors (2% to 40%). The model with the highest predictive capability explained 98% of the variation in FMWT data across regions, 70% of the variation in SKT data across regions and surveys, and 28% and 43% of the daily variation in salvage at federal and state fish screening facilities, respectively. The PEL estimate from this model was 35%, more than double the original estimate from Kimmerer (2008) of 15%. While PEL estimates provided in this study should be considered preliminary, our framework for testing combined behavior-driven movement models and population dynamics models is an improvement compared to earlier efforts.

Statistical Evaluation of Behavior and Population Dynamics Models Predicting Movement and Proportional Entrainment Loss of Adult Delta Smelt in the Sacramento–San Joaquin River Delta

There has been considerable debate about effects of entrainment of endangered Delta Smelt (Hypomesus transpacificus) at water export facilities located in the Sacramento–San Joaquin River Delta. In this paper we use a behavior-driven movement model (BMM) to simulate the movement of adult Delta Smelt, which, in conjunction with a population dynamics model, estimates the proportion of the population that is lost to entrainment, i.e., proportional entrainment loss (PEL). Parameters of the population model are estimated by maximum likelihood by comparing predictions to data from Fall Midwater Trawl (FMWT) and Spring Kodiak Trawl (SKT) surveys, as well as to daily salvage estimates. Our objectives are to evaluate different movement behavior hypotheses, to rank estimates of PEL based on how well predictions fit the data, and to sharpen our understanding of the data to inform future research and monitoring decisions. We applied the modeling framework to data from water year 2002—a year when salvage was high—and tested 30 combinations of six behavior and five population dynamics models. More complex process and observation assumptions in the population model led to much improved fits in most cases, but did not appreciably influence PEL predictions, which were largely determined by movement predictions from the BMMs. Estimates of PEL varied considerably among behaviors (2% to 40%). The model with the highest predictive capability explained 98% of the variation in FMWT data across regions, 70% of the variation in SKT data across regions and surveys, and 28% and 43% of the daily variation in salvage at federal and state fish screening facilities, respectively. The PEL estimate from this model was 35%, more than double the original estimate from Kimmerer (2008) of 15%. While PEL estimates provided in this study should be considered preliminary, our framework for testing combined behavior-driven movement models and population dynamics models is an improvement compared to earlier efforts.