Assessing Sediment Nutrient Storage and Release in California's Sacramento-San Joaquin Delta

Science Center Objects

Sediments represent an important pool of nutrients in the Sacramento-San Joaquin Delta (Delta). The exchange of nutrients between the water column and the benthos impacts water quality and effects phytoplankton, harmful algal blooms, aquatic vegetation, and drinking water quality. To date, there is very limited information about nutrient pools in Delta sediments, nor how these nutrients are transformed, stored or released. To address this, California Water Science Center scientists have begun the first comprehensive assessment of sediment nutrient inventories and fluxes in the Sacramento-San Joaquin Delta.

The study includes two overlapping components. Together, these two components will inform scientists of rates of nutrient processes across broad areas. This information will be available to Delta modelers to help build and validate process-based hydrologic-biogeochemical models.

The first component of the study is a survey of nutrient inventories in sediments across the Delta. Using a “paired site” approach that compares wetland/shallow water sites to nearby open water/channel sites, sediment samples will be collected and characterized at locations relevant to wetland restoration efforts, the spread of invasive aquatic vegetations, and changes in nutrient concentrations in overlying water associated with Regional San’s wastewater treatment plant upgrade (EchoWater Project - Regional San).

For the second component, at a subset of these locations additional information will be collected about benthic flux rates and microbial community structure and functional potential. Microorganisms mediate nutrient cycling in sediments, and recent metagenomic approaches offer new insights into ecosystem function. This will provide information about how sediment bulk properties and landscape scale factors affect the microbial community structure and concomitant sediment-water exchange of nutrients.


Biologist Ethan Enos

Biologist Ethan Enos holds up a core collected in the Delta.

Scientific Approach

The scientific approach to this project will be divided into several tasks. Included in these are broadscale sediment and targeted sediment sampling.

Broadscale sediment sampling

Under this task, sediment cores will be collected from over 20 locations across the Delta and Suisun Bay: at each location paired sites repressing channel/open water versus wetland/shallow water sites will be selected.  At each site, 4 to 6 cores will be collected and the top 1 cm of each core will be composited into one sample for analysis. Sediment samples will be analyzed to determine water content, bulk density, total carbon and nitrogen content, Olsen extractable phosphate, sediment grain size distribution, and readily available (water extractable) ammonium, nitrate, nitrite, dissolved organic nitrogen, carbon, and phosphate.

Targeted sediment sampling and in situ benthic flux measurements

At a subset of sites from the first task, nutrient flux rates to and from the sediment surface will be measured using an in situ flow-through benthic flux chamber. The chamber, which is about 1.2 meters diameter and holds about 60 liters, will be deployed from a boat. Changes in nutrient concentrations within the chamber will be measured by circulating water through an on-board system that measures nitrate, ammonium, and water quality parameters (e.g., temperature, conductance, turbidity), as well as dissolved organic matter and chlorophyll-a fluorescence. Sediment surface conditions will also be documented, using a continuous video feed from cameras mounted on the chamber.  Genomic analyses of  these sediments conducted in collaboration with researchers UC Davis will provide information about the microbial community including the presence of harmful cyanobacteria.

benthic flux chamber

This image shows the benthic flux chamber designed by the USGS California Water Science Center’s biogeochemistry group. The chamber is placed on the sediment surface and water is sealed in the chamber. The water is then carried to instruments on the boat that monitor changes in water quality over a period of 10 to 30 mins.

Timeline, Reporting, and Relevance

The planning phase of this will project will begin in the summer of 2019, with final reporting and other outreach activities culminating in the summer of 2023.

The USGS will process and oversee all sediment and water quality data collected and make them available to research partners as they become available.  As appropriate, data will be posted in the National Water Information System (NWIS) or in ScienceBase, where it will available to the public. High-frequency benthic flux measurements of nitrate, ammonium and other water-quality parameters may be provided in publicly available journal articles and/or posted in the USGS ScienceBase catalog. Scientists will prepare reports and journal articles describing the approaches developed and the identified relevant effects of nutrient storage and release in sediments and the overlying water column in the locations that were studied.

Findings from this project will be used to inform widescale wetland restoration efforts which are expected to change sediment nutrient inventories, transformation rates and fluxes which will impact Delta habitats. Findings will also serve as a baseline for assessing water quality improvements following upcoming upgrades to the Sacramento Regional County Sanitation District’s (Regional SAN’s) wastewater treatment plant biological nutrient removal upgrade in 2021.