Geology topics

Research about Sacramento–San Joaquin River Delta

Source-linked reports with geographic coverage including Sacramento–San Joaquin River Delta.

8 recordsLinked to original sources

USGS2024

Adult green sturgeon (Acipenser medirostris) movements in the Sacramento–San Joaquin River Delta, California, December 2020–January 2023

The U.S. Army Corps of Engineers American River Watershed Common Features project (ACRF) seeks to reduce flood risk for the City of Sacramento, California, and surrounding areas. The project includes levee-remediation measures to address seepage, stability, erosion, and height concerns as well as the widening of the Sacramento Weir and Bypass. The project reach is in the lower extent of the Sacramento River migration corridor for the federally threatened southern Distinct Population Segment of North American green sturgeon ( Acipenser medirostris ). To establish baseline migratory behavior, we examined adult green sturgeon transit through the project area prior to construction. Biologists from the U.S. Army Corps of Engineers collected and tagged 55 adult green sturgeon with acoustic and passive integrated transponders, near Hamilton City, California, at river kilometer 332 of the Sacramento River each fall from 2020 to 2022. To evaluate fish movements, we deployed five acoustic detection sites at river kilometers 101, 90, 76, and 21 on the Sacramento River and in Tule Canal near the Sacramento Bypass at river kilometer 101 of the Sacramento River. The acoustic receivers detected nearly all tagged fish moving downstream through the ARCF study area during the same water year (October 1–September 30) in which they were tagged. Three fish released in October of 2020 arrived at the ARCF study area more than 362 days later in October 2021. The timing of tagged fish movements was associated with increases in river flow and not hour of day. Adult green sturgeon moved downstream from January to August when streamflows exceeded 15,000 cubic feet per second. During water year 2023 and the critically dry water year 2022, fish moved with the first peaks in flow occurring from mid-October to early January. Fish tagged in the critically dry water year 2021 entered the ARCF study area over an extended period from January to October, when flows remained around 10,000 cubic feet per second all year. Fish moved quickly between sites within the ARCF study area and generally spent less than 1 hour at each detection site.

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USGS2021

Juvenile Chinook salmon survival, travel time, and floodplain use relative to riverine channels in the Sacramento–San Joaquin River Delta

Floodplains provide multiple benefits to both resident and migratory fish species, including juvenile Chinook Salmon Oncorhynchus tshawytscha , but direct comparisons of survival during migration through a floodplain versus riverine routes are scarce. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 30% of years in response to large, uncontrolled runoff events. We analyzed data from an acoustic telemetry study conducted in winter 2016 to estimate the proportion of tagged juvenile Chinook Salmon entrained from the Sacramento River into the Yolo Bypass and their spatial distribution within the Yolo Bypass. In addition, we compared survival and travel time of Chinook Salmon that migrated through the Yolo Bypass to those migrating via alternative non‐floodplain migration routes at varying stages of a flood event that activated the Yolo Bypass. We found that entrainment into the Yolo Bypass ranged from 1% to 80% among different release groups, with the highest entrainment coinciding with the peak of the March 2016 flooding event. Survival for Chinook Salmon migrating through the Yolo Bypass was similar to survival of those migrating through main‐stem migration routes. At the relatively high flows necessary to enable flooding of the Yolo Bypass, survival estimates varied little among release groups and migration routes. Furthermore, mean daily survival rates for Chinook Salmon migrating through the flooded Yolo Bypass were comparable to those of fish migrating through the other non‐floodplain routes. Median travel times remained relatively constant during various stages of flooding in the Yolo Bypass. This research should help managers to better understand the potential costs and benefits to floodplain restoration and routing of migrating Chinook Salmon into off‐channel habitat.

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USGS2020

Fish predation on a landscape scale

Predator–prey dynamics can have landscape-level impacts on ecosystems, and yet, spatial patterns and environmental predictors of predator–prey dynamics are often investigated at discrete locations, limiting our understanding of the broader impacts. At these broader scales, landscapes often contain multiple complex and heterogeneous habitats, requiring a spatially representative sampling design. This challenge is especially pronounced in California’s Sacramento–San Joaquin River Delta, where managers require information on the landscape-scale impacts of non-native fish predators on multiple imperiled native prey fish populations. We quantified relative predation risk in the southern half of the Delta (South Delta) in 2017 using floating baited tethers that record the exact time and location of predation events. We selected 20 study sites using a generalized random tessellation stratified survey design, which allowed us to infer relationships between key environmental covariates and predation across a broader spatial scale than previous studies. Covariates included distance-to-nearest predators, water temperature, turbidity, depth, bottom slope, bottom roughness, water velocity, and distance-to-nearest riverbank and nearest aquatic vegetation bed. Model selection determined the covariates that best predicted relative predation risk: water temperature, time of day, mean predator distance, and river bottom roughness. Using this model, we estimated predation risk for the South Delta landscape at a 1-day and 1-km resolution. This effort identified hot spots of predation risk and allowed us to generate predicted survival for migrating fish transiting the South Delta. This methodology can be applied to other systems to evaluate spatio-temporal dynamics in predation risk, and their biotic and abiotic predictors.

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USGS2018

Flow-mediated effects on travel time, routing, and survival of juvenile Chinook salmon in a spatially complex, tidally forced river delta

We evaluated the interacting influences of river flows and tides on travel time, routing, and survival of juvenile late-fall Chinook salmon ( Oncorhynchus tshawytscha ) migrating through the Sacramento–San Joaquin River Delta. To quantify these effects, we jointly modeled the travel time, survival, and migration routing in relation to individual time-varying covariates of acoustic-tagged salmon within a Bayesian framework. We used observed arrival times for detected individuals and imputed arrival times for undetected individuals to assign covariate values in each reach. We found travel time was inversely related to river inflow in all reaches, yet survival was positively related to inflow only in reaches that transitioned from bidirectional tidal flows to unidirectional flow with increasing inflows. We also found that the probability of fish entering the interior Delta, a low-survival reach, declined as inflow increased. Our study illustrates how river inflows interact with tides to influence fish survival during the critical transition between freshwater and ocean environments. Furthermore, our analytical framework introduces new techniques to integrate formally over missing covariate values to quantify effects of time-varying covariates.

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USGS2016

Recent advances in understanding flow dynamics and transport of water-quality constituents in the Sacramento–San Joaquin River Delta

This paper, part of the collection of research comprising the State of Bay–Delta Science 2016, describes advances during the past decade in understanding flow dynamics and how water-quality constituents move within California’s Sacramento– San Joaquin River Delta (Delta). Water-quality constituents include salinity, heat, oxygen, nutrients, contaminants, organic particles, and inorganic particles. These constituents are affected by water diversions and other human manipulations of flow, and they greatly affect the quantity and quality of benthic, pelagic, and intertidal habitat in the Delta. The Pacific Ocean, the Central Valley watershed, human intervention, the atmosphere, and internal biogeochemical processes are all drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments deployed in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain pelagic habitat and tidal marsh, especially as sea level rises. Connections among the watershed, Delta, and San Francisco Bay that have been quantified recently highlight that a landscape view of this system is needed, rather than consideration of each region in isolation. We discuss interactions of multiple drivers and information gaps.

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USGS2015

Effect of tides, river flow, and gate operations on entrainment of juvenile salmon into the interior Sacramento–San Joaquin River Delta

Juvenile Chinook Salmon Oncorhynchus tshawytscha emigrating from natal tributaries of the Sacramento River, California, must negotiate the Sacramento-San Joaquin River Delta (hereafter, the Delta), a complex network of natural and man-made channels linking the Sacramento River with San Francisco Bay. Fish that enter the interior and southern Delta—the region to the south of the Sacramento River where water pumping stations are located—survive at a lower rate than fish that use alternative migration routes. Consequently, total survival decreases as the fraction of the population entering the interior Delta increases, thus spurring management actions to reduce the proportion of fish that are entrained into the interior Delta. To better inform management actions, we modeled entrainment probability as a function of hydrodynamic variables. We fitted alternative entrainment models to telemetry data that identified when tagged fish in the Sacramento River entered two river channels leading to the interior Delta (Georgiana Slough and the gated Delta Cross Channel). We found that the probability of entrainment into the interior Delta through both channels depended strongly on the river flow and tidal stage at the time of fish arrival at the river junction. Fish that arrived during ebb tides had a low entrainment probability, whereas fish that arrived during flood tides (i.e., when the river's flow was reversed) had a high probability of entering the interior Delta. We coupled our entrainment model with a flow simulation model to evaluate the effect of nighttime closures of the Delta Cross Channel gates on the daily probability of fish entrainment into the interior Delta. Relative to 24-h gate closures, nighttime closures increased daily entrainment probability by 3 percentage points on average if fish arrived at the river junction uniformly throughout the day and by only 1.3 percentage points if 85% of fish arrived at night. We illustrate how our model can be used to evaluate the effects of alternative water management actions on fish entrainment into the interior Delta.

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USGS2003

Phytoplankton fuels Delta food web

Populations of certain fishes and invertebrates in the Sacramento-San Joaquin Delta have declined in abundance in recent decades and there is evidence that food supply is partly responsible. While many sources of organic matter in the Delta could be supporting fish populations indirectly through the food web (including aquatic vegetation and decaying organic matter from agricultural drainage), a careful accounting shows that phytoplankton is the dominant food source. Phytoplankton, communities of microscopic free-floating algae, are the most important food source on a Delta-wide scale when both food quantity and quality are taken into account. These microscopic algae have declined since the late 1960s. Fertilizer and pesticide runoff do not appear to be playing a direct role in long-term phytoplankton changes; rather, species invasions, increasing water transparency and fluctuations in water transport are responsible. Although the potential toxicity of herbicides and pesticides to plank- ton in the Delta is well documented, the ecological significance remains speculative. Nutrient inputs from agricultural runoff at current levels, in combination with increasing transparency, could result in harmful algal blooms.

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USGS2002

Functional variability of habitats within the Sacramento-San Joaquin Delta: Restoration implications

We have now entered an era of large-scale attempts to restore ecological functions and biological communities in impaired ecosystems. Our knowledge base of complex ecosystems and interrelated functions is limited, so the outcomes of specific restoration actions are highly uncertain. One approach for exploring that uncertainty and anticipating the range of possible restoration outcomes is comparative study of existing habitats similar to future habitats slated for construction. Here we compare two examples of one habitat type targeted for restoration in the Sacramento-San Joaquin River Delta. We compare one critical ecological function provided by these shallow tidal habitats - production and distribution of phytoplankton biomass as the food supply to pelagic consumers. We measured spatial and short-term temporal variability of phytoplankton biomass and growth rate and quantified the hydrodynamic and biological processes governing that variability. Results show that the production and distribution of phytoplankton biomass can be highly variable within and between nearby habitats of the same type, due to variations in phytoplankton sources, sinks, and transport. Therefore, superficially similar, geographically proximate habitats can function very differently, and that functional variability introduces large uncertainties into the restoration process. Comparative study of existing habitats is one way ecosystem science can elucidate and potentially minimize restoration uncertainties, by identifying processes shaping habitat functionality, including those that can be controlled in the restoration design.

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