Effects of Aquatic Vegetation on Water Quality and Residence Time in the Bay-Delta

Science Center Objects

The spread of invasive aquatic vegetation in the Sacramento-San Joaquin Delta is having a profound impact on the Delta’s natural habitat. The presence of these “aquatic weeds” has been shown to alter water velocity and increase water clarity, posing threats to native fish species, specifically the threatened Delta Smelt. These aquatic plants can also affect the foodweb by altering nutrient, phytoplankton, and zooplankton dynamics, impacting both local and downstream conditions.

aerial view of bay-delta region

This is an aerial view of the bay-delta region in California (Public domain)

To better understand the effects of aquatic weeds on Delta habitats, the California Department of Water Resources (DWR), in collaboration with the California State Parks Division of Boating and Waterways (DBW), the USGS, and other agencies, is conducting a multi-year study in the Cache Slough Complex located in the northern Delta. As part of this study, two wetland habitats will be compared: (1) Little Hastings Tract which will be treated with herbicides and (2) French Island which will serve as an untreated control. Both sites will be monitored for physical, chemical, and biological parameters to inform management as to whether habitat attributes relevant to Delta Smelt change favorably for the species when aquatic vegetation is treated with herbicide.

This work is proceeding as part of the multi-agency Delta Smelt Resiliency Strategy.


In support of the effort to understand the effects of invasive aquatic vegetation on habitat quality and evaluate the effectiveness and benefits of herbicide applications, the USGS California Water Science Center team will collect spatially and temporally dense water quality measurements in both the treated (Little Hastings Tract) and untreated (French Island) sites that are part of this study. Using the USGS’s novel boat-based, flow-through high frequency instrument set-up, in situ measurements will be collected for temperature, conductivity, dissolved oxygen, pH, turbidity, chlorophyll-a, nitrate, ammonium, and stable isotopes of water. Additional data will be analyzed from discrete water samples collected in tandem.

herbicide coverage area map of bay-delta

Herbicide coverage area map of bay-delta (Public domain)

The data obtained from these efforts will help determine whether there are differences between treated versus untreated sites, as well as differences across the sites that can be attributed to aquatic vegetation biomass and species composition. This information will also be used to validate hydrodynamic models and put water quality data collected by DWR into a greater spatial context. In addition, the information can be used to interpret the airborne flyover data collected as part of this study.

Science Plan

Spatial (horizontal and vertical) and seasonal variability in water quality constituents will be measured using a boat-mounted flow-through sampling system. Each data point will be associated with a time, depth, and GPS location. Data will be viewed on the boat in real time to enable operators to make immediate decisions about data collection and assess instrument performance.

The boatbased flow-through system will be modified such that the intake tube can be utilized to collect continuous vertical profiles. The intake tube will be equipped with a depth sensor so that water quality data can be associated not only with a specific date, time, latitude and longitude, but also with a specific water depth. If this approach does not work under all conditions, a multiparameter YSI EXO 2 sonde and SUNA (for nitrate) will be slowly lowered into the water to collect vertical profiles of at least a subset of parameters (Table 1). 

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