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Research about Sacramento River

Source-linked reports with geographic coverage including Sacramento River.

At least 19 recordsLinked to original sources

Development and field testing of a UAS-based software-defined radar for measuring freshwater bathymetry

We provide an overview of an uncrewed aircraft system (UAS)-based software-defined radar (SDRadar) system for high-resolution geophysical observations. The radar transceiver is implemented on a Radio Frequency System-on-Chip (RFSoC) platform, along with an ultra-wideband Vivaldi antenna that has a starting operating frequency of 150 MHz, enabling the system to be used across different applications, including measurements of freshwater bathymetry. In addition to system design and subsystem performance assessments, this paper presents the results of field testing conducted along the Sacramento River near Glenn, California, USA. The radar-derived river depth measurements are compared with ground truth data collected from a crewed boat using an acoustic Doppler current profiler (ADCP). The results show good agreement, with a root mean square error (RMSE) of 0.079 m.

California

Mapping river flow from thermal images in approximately real time: Proof of concept on the Sacramento River, California, USA

Image velocimetry has become an effective method of mapping flow conditions in rivers, but this analysis is typically performed in a post-processing mode after data collection is complete. In this study, we evaluated the potential to infer flow velocities in approximately real time as thermal images are being acquired from an uncrewed aircraft system (UAS). The sensitivity of thermal image velocimetry to environmental conditions was quantified by conducting 20 flights over four days and assessing the accuracy of image-derived velocity estimates via comparison to direct field measurements made with an acoustic Doppler current profiler (ADCP). This analysis indicated that velocity mapping was most reliable when the air was cooler than the water. We also introduced a workflow for River Velocity Measurement in Approximately Real Time (RiVMART) that involved transferring brief image sequences from the UAS to a ground station as distinct data packets. The resulting velocity fields were as accurate as those generated via post-processing. A new particle image velocimetry (PIV) algorithm based on staggered image sequences increased the number of image pairs available for a given image sequence duration and slightly improved accuracy relative to a standard PIV implementation. Direct, automated geo-referencing of image-derived velocity vectors based on information on the position and orientation of the UAS acquired during flight led to poor alignment with vectors that were geo-referenced manually by selecting ground control points from an orthophoto. This initial proof-of-concept investigation suggests that our workflow could enable highly efficient characterization of flow fields in rivers and might help support applications that require rapid response to changing conditions.

California

Evaluating the potential for efficient, UAS-based reach-scale mapping of river channel bathymetry from multispectral images

Introduction: Information on spatial patterns of water depth in river channels is valuable for numerous applications, but such data can be difficult to obtain via traditional field methods. Ongoing developments in remote sensing technology have enabled various image-based approaches for mapping river bathymetry; this study evaluated the potential to retrieve depth from multispectral images acquired by an uncrewed aircraft system (UAS). Methods: More specifically, we produced depth maps for a 4 km reach of a clear-flowing, relatively shallow river using an established spectrally based algorithm, Optimal Band Ratio Analysis. To assess accuracy, we compared image-derived estimates to direct measurements of water depth. The field data were collected by wading and from a boat equipped with an echo sounder and used to survey cross sections and a longitudinal profile. We partitioned our study area along the Sacramento River, California, USA, into three distinct sub-reaches and acquired a separate image for each one. In addition to the typical, self-contained, per-image depth retrieval workflow, we also explored the possibility of exporting a relationship between depth and reflectance calibrated using data from one site to the other two sub-reaches. Moreover, we evaluated whether sampling configurations progressively more sparse than our full field survey could still provide sufficient calibration data for developing robust depth retrieval models. Results: Our results indicate that under favorable environmental conditions like those observed on the Sacramento River during low flow, accurate, precise depth maps can be derived from images acquired by UAS, not only within a sub-reach but also across multiple, adjacent sub-reaches of the same river. Discussion: Moreover, our findings imply that the level of effort invested in obtaining field data for calibration could be significantly reduced. In aggregate, this investigation suggests that UAS-based remote sensing could facilitate highly efficient, cost-effective, operational mapping of river bathymetry at the reach scale in clear-flowing streams.

California

Sacramento River nutrient change study

The Sacramento River Nutrient Change Study (SRiNCS) was developed with input from multiple stakeholders in the Delta Regional Monitoring Program, as well as the State Water Contractors. We tracked the effects of changes in nutrient loading resulting from a short-term wastewater hold at the Sacramento River Wastewater Treatment Plant (SRWTP). In the summer of 2019, scheduled wastewater effluent holds occurred during the Effluent Valve Replacement (EVR) project, part of the EchoWater Project upgrade at the SRWTP. During an EVR hold in early September 2019, no treated effluent entered the Sacramento River for 48 hours, creating a parcel of “without-wastewater” river water approximately 20 miles (32 km) long. We observed the magnitudes and impacts of short-term changes in nutrient loading in water with wastewater (WW+, September 10) and without wastewater (WW-, September 11 and 12) in the Sacramento River and three downstream channels: Georgiana Slough, the North Fork Mokelumne River, and the South Fork Mokelumne River

California

Evaluating the sensitivity of multi-dimensional model predictions of salmon habitat to the source of remotely sensed river bathymetry

Multi-dimensional numerical models are fundamental tools for investigating biophysical processes in aquatic ecosystems. Remote sensing techniques increase the feasibility of applying such models at riverscape scales, but tests of model performance on large rivers have been limited. We evaluated the potential to develop two-dimensional (2D) and three-dimensional (3D) hydrodynamic models for a 1.6-km reach of a large gravel-bed river using three sources of remotely sensed river bathymetry. We estimated depth from hyperspectral image data acquired from conventional and uncrewed aircraft and multispectral satellite imagery. Our results indicated that modeled water depth errors were similar between 2D and 3D models, with depth residuals that were comparable to the uncertainty associated with the bathymetry used as input. We found good agreement between measured and modeled depth-averaged velocities generated by 2D and 3D models, while 3D models provided superior predictions of near-bed velocities. We found that optimal model performance occurred for lower flow resistance values than previously reported in the literature, possibly as a consequence of the high-resolution bathymetry used as model input. Model predictions of winter-run Chinook salmon ( Oncorhynchus tshawytscha ) spawning and rearing habitat were not sensitive to the source of bathymetric information, but bioenergetic predictions related to adult holding costs were influenced by the input bathymetry. Our results suggest that hyperspectral imagery acquired from piloted and/or uncrewed aircraft can be used to map the bathymetry of clear-flowing, relatively shallow large rivers with sufficient accuracy to support multi-dimensional flow model development; models developed from multispectral satellite imagery had more limited predictive capability.

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Factors affecting spatiotemporal variation in survival of endangered winter-run Chinook Salmon outmigrating from the Sacramento River

Among four extant and declining Chinook salmon ( Oncorhynchus tshawytscha) runs in California’s Central Valley, none have declined as precipitously as Sacramento River winter-run Chinook Salmon. In addition to habitat loss, migratory winter-run employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. This life history strategy is widely considered to be a key factor in the continued decline of winter-run. Using acoustic telemetry, we examined conditions that influenced reach-specific movement and survival of outmigrating juveniles during a prolonged, multi-year drought from 2013-2016, followed by one of the wettest years on record in 2017. We modeled how time-varying individual riverine covariates and reach-specific habitat features influenced smolt survival. Model selection favored a model with mean annual flow, intra-annual deviations from the mean flow at the reach scale, reach-specific channel characteristics, and travel time. Mean annual flow had the strongest positive effect on survival. A negative interaction between mean annual flow and intra-annual reach flow indicated that within-year deviations at the reach scale from annual mean flow had larger effects on survival in low flow years. These factors resulted in higher survival in years with pulse flows or high flows. Changes in movement behavior in response to small scale changes in velocity were negatively associated with survival. Covariates of revetment and wooded bank habitat were positively associated with survival but the effect of these fixed habitat features changed depending on whether they were situated in the upper or lower part of the river. Fish exhibited density dependent stopover behavior, with slowed downstream migration in the upper river in the wet years and extending to the lower river in the most critically dry year. This paper contributes two key findings for natural resource managers interested in flow management and targeted habitat restoration. The first is new insight to how the magnitude of pulse flows in dry and wet years affect survival of winter-run. The second is that density dependence influences where stopover habitat is used. Despite this, we identified an area of the river where fish consistently exhibited stopover behavior in all years.

California

From drought to deluge: Spatiotemporal variation in migration routing, survival, travel time and floodplain use of an endangered migratory fish

We developed a novel statistical model to relate the daily survival and migration dynamics of an endangered anadromous fish to river flow and water temperature during both extreme drought and severe flooding in an intensively managed river system. Our Bayesian temporally stratified multistate mark recapture model integrates over unobserved travel times and route transitions to efficiently estimate covariate relationships and includes an adjustment for telemetry tag battery failure. We applied the model to acoustic-tagged juvenile Sacramento river winter-run Chinook salmon (Oncorhynchus tshawytscha) and found that survival decreased with decreasing river flows and increased water temperatures. We found that fish were likely to enter at a large floodplain during flood conditions and that survival in floodplain was comparable to the mainstem Sacramento river. Our study demonstrates the response of an endangered anadromous fish population to extreme spatial and temporal variability in habitat accessibility and quality. The general model framework we introduce here can be applied to telemetry of migratory fish through systems with multiple routes to efficiently estimate spatiotemporal variation in survival, travel time, and routing.

California

Sacramento pikeminnow migration record

Sacramento Pikeminnow Ptychocheilus grandis is a potamodromous species endemic to mid- and low-elevation streams and rivers of Central and Northern California. Adults are known to undertake substantial migrations, typically associated with spawning, though few data exist on the extent of these migrations. Six Sacramento Pikeminnow implanted with passive integrated transponder tags in the Sacramento–San Joaquin Delta were detected in Cottonwood and Mill creeks, tributaries to the Sacramento River in Northern California, between April 2018 and late February 2020. Total travel distances ranged from 354 to 432 km, the maximum of which exceeds the previously known record by at least 30 km. These observations add to a limited body of knowledge regarding the natural history of Sacramento Pikeminnow and highlight the importance of the river–estuary continuum as essential for this migratory species.

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Remote sensing of river bathymetry: Evaluating a range of sensors, platforms, and algorithms on the upper Sacramento River, California, USA

Remote sensing has become an increasingly viable tool for characterizing fluvial systems. In this study, we used field measurements from a 1.6 km reach of the upper Sacramento River, CA, to evaluate the potential of mapping water depths from a range of platforms, sensors, and depth retrieval methods. Field measurements of water column optical properties also were compared to similar data sets from other rivers to provide context for our results. We considered field spectra, a multispectral satellite image, hyperspectral data collected from conventional and unmanned aircraft, and a bathymetric LiDAR and applied a generalized version of Optimal Band Ratio Analysis (OBRA) and the K nearest neighbors regression (KNN) machine learning algorithm. Linear, quadratic, exponential, power, and lowess OBRA models enabled more flexible curve-fitting in calibrating spectrally based quantities to depth; an exponential formulation avoided artifacts associated with other model types. KNN increased observed vs. predicted R2 values, particularly for the satellite image; we also found that pre-processing of satellite images was unnecessary and that a basic data product could be used for depth retrieval. Bathymetric LiDAR was highly accurate and precise in shallow water, but a lack of bottom returns from areas greater than 2 m deep resulted in large gaps in coverage. The maximum detectable depth imposes an important constraint on fluvial remote sensing and a hybrid approach combined with field surveys of deep areas might be a more realistic operational strategy for bathymetric mapping. Future work will focus on scaling up from short reaches to long river segments.

California

Estimating spatial–temporal differences in Chinook salmon outmigration survival with habitat- and predation-related covariates

Low survival rates of Chinook salmon ( Oncorhynchus tshawytscha ) smolts in California’s Central Valley have been attributed to multiple biological and physical factors, but it is not clear which factors have the largest impact. We used 5 years of acoustic telemetry data for 1709 late-fall Chinook salmon smolts to evaluate the effect of habitat- and predation-related covariates on outmigration survival through the Sacramento River. Using a Cormack–Jolly–Seber mark–recapture model, we estimated survival rates both as a function of covariates (covariate model) and as a function of river location and release year (spatial–temporal model). Our covariate model was overwhelmingly supported as the preferred model based on model selection criteria, suggesting the covariates adequately replicated spatial and temporal patterns in smolt survival. The covariates in the selected model included individual fish covariates, habitat-specific covariates, and temporally variable physical conditions. The most important covariate affecting salmon survival was flow. We describe the importance of these parameters in the context of juvenile salmon predation risk and suggest that additional research on predator distribution and density could improve model estimates.

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Hydrology and hydrodynamics on the Sacramento River near the Fremont Weir, California—Implications for juvenile salmon entrainment estimates

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the weir to increase access to the Yolo Bypass, a seasonal floodplain of the Sacramento River. Detailed hydrodynamic and velocity measurements were made at a river bend near the Fremont Weir in the winter and spring of 2016 to examine backwater conditions and estimate the hydraulic entrainment zone, a zone where fish would be predicted to be entrained into the notch. Secondary circulation near the river bend was shown to shift the velocity and discharge distributions toward the outside of the bend. Variability in the stage-discharge relation was shown to be the biggest source of uncertainty in determining the location of the hydraulic entrainment zone. Outflow from the Sutter Bypass and high flow on the Feather River resulted in backwater conditions near the Fremont Weir about 25 percent of the time over the 27-year period from April 1990–April 2017. Velocity measurements used to estimate the critical streakline position (the outer edge of the hydraulic entrainment zone) were not made over a sufficient range of conditions to explicitly quantify the variability in the location of the critical streakline. The variability in the critical streakline position was therefore represented stochastically with a random effects model. The estimated position of the critical streakline and the random effects model are input parameters used in a simulation designed to estimate fish entrainment over a 15-year period. The estimates of the critical streakline and likely fish entrainment could be much improved with velocity measurements over a broader range of stage and discharge conditions.

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Use of flow cytometry and stable isotope analysis to determine phytoplankton uptake of wastewater derived ammonium in a nutrient-rich river

Anthropogenic alteration of the form and concentration of nitrogen (N) in aquatic ecosystems is widespread. Understanding availability and uptake of different N sources at the base of aquatic food webs is critical to establishment of effective nutrient management programs. Stable isotopes of N ( 14 N, 15 N) are often used to trace the sources of N fueling aquatic primary production, but effective use of this approach requires obtaining a reliable isotopic ratio for phytoplankton. In this study, we tested the use of flow cytometry to isolate phytoplankton from bulk particulate organic matter (POM) in a portion of the Sacramento River, California, during river-scale nutrient manipulation experiments that involved halting wastewater discharges high in ammonium (NH 4 + ). Field samples were collected using a Lagrangian approach, allowing us to measure changes in phytoplankton N source in the presence and absence of wastewater-derived NH 4 + . Comparison of δ 15 N-POM and δ 15 N-phytoplankton ( δ 15 N-PHY) revealed that their δ 15 N values followed broadly similar trends. However, after 3 days of downstream travel in the presence of wastewater treatment plant (WWTP) effluent, δ 15 N-POM and δ 15 N-PHY in the Sacramento River differed by as much as 7 ‰. Using a stable isotope mixing model approach, we estimated that in the presence of effluent between 40 and 90 % of phytoplankton N was derived from NH 4 + after 3 days of downstream transport. An apparent gradual increase over time in the proportion of NH 4 + in the phytoplankton N pool suggests that either very low phytoplankton growth rates resulted in an N turnover time that exceeded the travel time sampled during this study, or a portion of the phytoplankton community continued to access nitrate even in the presence of elevated NH 4 + concentrations.

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Fine-scale habitat preference of green sturgeon (Acipenser medirostris) within three spawning locations in the Sacramento River, California

Vast sections of the Sacramento River have been listed as critical habitat by the National Marine Fisheries Service for green sturgeon spawning ( Acipenser medirostris ), yet spawning is known to occur at only a few specific locations. This study reveals the range of physical habitat variables selected by adult green sturgeon during their spawning period. We integrated fine-scale fish positions, physical habitat characteristics, discharge, bathymetry, and simulated velocity and depth using a 2-dimensional hydraulic model (FaSTMECH). The objective was to create habitat suitability curves for depth, velocity, and substrate type within three known spawning locations over two years. An overall cumulative habitat suitability score was calculated that averaged the depth, velocity, and substrate scores over all fish, sites, and years. A weighted usable area (WUA) index was calculated throughout the sampling periods for each of the three sites. Cumulative results indicate that the microhabitat characteristics most preferred by green sturgeon in these three spawning locations were velocities between 1.0-1.1 m/s, depths of 8-9 m, and gravel and sand substrate. This study provides guidance for those who may in the future want to increase spawning habitat for green sturgeon within the Sacramento River.

California

Using paired in situ high frequency nitrate measurements to better understand controls on nitrate concentrations and estimate nitrification rates in a wastewater-impacted river

We used paired continuous nitrate ( ) measurements along a tidally affected river receiving wastewater discharge rich in ammonium ( ) to quantify rates of change in concentration ( ) and estimate nitrification rates. sensors were deployed 30 km apart in the Sacramento River, California (USA), with the upstream station located immediately above the regional wastewater treatment plant (WWTP). We used a travel time model to track water transit between the stations and estimated every 15 min (October 2013 to September 2014). Changes in concentration were strongly related to water temperature. In the presence of wastewater, was generally positive, ranging from about 7 µ M d −1 in the summer to near zero in the winter. Numerous periods when the WWTP halted discharge allowed the to be estimated under no-effluent conditions and revealed that in the absence of effluent, net gains in were substantially lower but still positive in the summer and negative (net sink) in the winter. Nitrification rates of effluent-derived NH 4 ( ) were estimated from the difference between measured in the presence versus absence of effluent and ranged from 1.5 to 3.4 µ M d −1 , which is within literature values but tenfold greater than recently reported for this region. was generally lower in winter (∼2 µ M d −1 ) than summer (∼3 µ M d −1 ). This in situ, high frequency approach provides advantages over traditional discrete sampling, incubation, and tracer methods and allows measurements to be made over broad areas for extended periods of time. Incorporating this approach into environmental monitoring programs can facilitate our ability to protect and manage aquatic systems.

California

Science advancements key to increasing management value of life stage monitoring networks for endangered Sacramento River winter-run Chinook salmon in California

A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winterrun Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues.

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A river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium

Phytoplankton are critical component of the food web in most large rivers and estuaries, and thus identifying dominant controls on phytoplankton abundance and species composition is important to scientists, managers, and policymakers. Recent studies from a variety of systems indicate that ammonium ( NH + 4 ) in treated wastewater effluent decreases primary production and alters phytoplankton species composition. However, these findings are based mainly on laboratory and enclosure studies, which may not adequately represent natural systems. To test effects of effluent high in ammonium on phytoplankton at the ecosystem scale, we conducted whole-river–scale experiments by halting discharges to the Sacramento River from the regional wastewater treatment plant (WWTP), and used a Lagrangian approach to compare changes in phytoplankton abundance and species composition in the presence (+EFF) and absence (−EFF) of effluent. Over 5 d of downstream travel from 20 km above to 50 km below the WWTP, chlorophyll concentrations declined from 15–25 to ∼2.5 μg L −1 , irrespective of effluent addition. Benthic diatoms were dominant in most samples. We found no significant difference in phytoplankton abundance or species composition between +EFF and −EFF conditions. Moreover, greatest declines in chlorophyll occurred upstream of the WWTP where NH + 4 concentrations were low. Grazing by clams and zooplankton could not account for observed losses, suggesting other factors such as hydrodynamics and light limitation were responsible for phytoplankton declines. These results highlight the advantages of conducting ecosystem-scale, Lagrangian-based experiments to understand the dynamic and complex interplay between physical, chemical, and biological factors that control phytoplankton populations.

California

Identifying when tagged fishes have been consumed by piscivorous predators: application of multivariate mixture models to movement parameters of telemetered fishes

Background Consumption of telemetered fishes by piscivores is problematic for telemetry studies because tag detections from the piscivore could introduce bias into the analysis of telemetry data. We illustrate the use of multivariate mixture models to estimate group membership (smolt or predator) of telemetered juvenile Chinook salmon ( Oncorhynchus tshawytscha ), juvenile steelhead trout ( O. mykiss ), striped bass ( Morone saxatilis ), smallmouth bass ( Micropterus dolomieu ) and spotted bass ( M. punctulatus ) in the Sacramento River, CA, USA. First, we estimated two types of track statistics from spatially explicit two-dimensional movement tracks of telemetered fishes: the Lévy exponent ( b ) and tortuosity ( τ ). Second, we hypothesized that the distribution of each track statistic would differ between predators and smolts. To estimate the distribution of track statistics for putative predators and smolts, we fitted a bivariate normal mixture model to the mixed distribution of track statistics. Lastly, we classified each track as a smolt or predator using parameter estimates from the mixture model to estimate the probability that each track was that of a predator or smolt. Results Tracks classified as predators exhibited movement that was tortuous and consistent with prey searching tactics, whereas tracks classified as smolts were characterized by directed, linear downstream movement. The estimated mean tortuosity was 0.565 (SD = 0.07) for predators and 0.944 (SD = 0.001) for smolts. The estimated mean Lévy exponent was 1.84 (SD = 1.23) for predators and -0.304 (SD = 1.46) for smolts. We correctly classified 90% of the Micropterus species and 72% of the striped bass as predators. For tagged smolts, 80% of Chinook salmon and 74% of steelhead trout were not classified as predators. Conclusions Mixture models proved valuable as a means to differentiate between salmonid smolts and predators that consumed salmonid smolts. However, successful application of this method requires that telemetered fishes and their predators exhibit measurable differences in movement behavior. Our approach is flexible, allows inclusion of multiple track statistics and improves upon rule-based manual classification methods.

California

Trends in the sediment yield of the Sacramento River, California, 1957-2001

Human activities within a watershed, such as agriculture, urbanization, and dam building, may affect the sediment yield from the watershed. Because the equilibrium geomorphic form of an estuary is dependent in part on the sediment supply from the watershed, anthropogenic activities within the watershed have the potential to affect estuary geomorphology. The Sacramento River drains the northern half of California’s Central Valley and is the primary source of sediment to San Francisco Bay. In this paper, it is shown that the delivery of suspended-sediment from the Sacramento River to San Francisco Bay has decreased by about one-half during the period 1957 to 2001. Many factors may be contributing to the trend in sediment yield, including the depletion of erodible sediment from hydraulic mining in the late 1800s, trapping of sediment in reservoirs, riverbank protection, altered land-uses (such as agriculture, grazing, urbanization, and logging), and levees. This finding has implications for planned tidal wetland restoration activities around San Francisco Bay, where an adequate sediment supply will be needed to build subsided areas to elevations typical of tidal wetlands as well as to keep pace with projected sea-level rise. In a broader context, the study underscores the need to address anthropogenic impacts on watershed sediment yield when considering actions such as restoration within downstream depositional areas.

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