Monitoring Cyanotoxins in California's Sacramento-San Joaquin Delta: Fixed Stations and High-Resolution Mapping Surveys

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California’s Sacramento-San Joaquin River Delta (Delta) provides drinking water to about 30 million people and irrigation water to the agriculturally rich Central Valley. The Delta is also home to numerous threatened and endangered native species. The health of the Delta's aquatic ecosystems, and fish in particular, have long been in a state of decline. This is associated with decreasing phytoplankton productivity and a shift in species composition.

Flakes of microcystis floating in the water of the southern Delta

This photo shows flakes of microcystis, a genus of freshwater cyanobacteria, floating in the water of the southern Delta.​​​​​​​ (Click to enlarge.)

Over the past decade there also have been increases in harmful algal blooms (HABs). While some HABs are nontoxic, others contain cyanobacteria which may produce dangerous toxins (cyanotoxins) that pose a health threat to people and animals. Previous studies have shown cyanotoxins to be common in many of California’s streams and reservoirs, but less is known about the hydrodynamically complex Delta.

To help quantify levels of cyanotoxins in the Delta, USGS scientists will use a combination of monitoring at fixed stations equipped with in situ sensors that monitor flow and water quality continuously (every 15 minutes) and will also employ a novel high-resolution, boat-based mapping survey system. The boat-based approach involves flowing water while underway (~25 mph) through an on-board instrument system that measures multiple water quality parameters every second. The goal is to collect flow, water quality, and cyanotoxin data in a way that will help us understand the drivers of HABs and cyanotoxin production and transport.


Fixed Station Monitoring

The USGS California Water Science Center (CAWSC) runs a network of water quality monitoring stations in the Delta. These stations are equipped with sensors that measure flow, physico-chemical properties (temperature, specific conductance, turbidity, pH, dissolved oxygen), nitrate, and phytoplankton abundance (chlorophyll-a fluorescence). In addition, under a separately funded study, these stations will be equipped with bbe FluoroProbes that measure not only phytoplankton abundance but also phytoplankton species distribution (cyanobacteria, diatoms, cryptophytes, green algae). The addition of cyanotoxin data collection – using both discrete water sampling and deployment of Solid Phase Adsorption Toxin Tracking (SPATT) samplers – to these stations will provide insight into drivers, sources, and transport of HABs and associated cyanotoxins.

Map showing Bay-Delta cyanotoxin study area

These maps show the two methods of data collection for this study. Map A shows continuous water quality fixed monitoring stations (points) and the two stations (stars) where whole water and SPATT samples will be collected . Map B shows the area covered by the boat-based mapping surveys. Color gradient shows variation in the percent of the total chlorophyll-a pool attributed to cyanobacteria (aka blue-green algae) measured using a bbe FluoroProbe during 2018 USGS surveys, with yellow and orange indicating higher concentrations. 

Boat-Based Mapping

The boat-based approach will add cyanotoxin measurement to other water-quality data collected during mapping surveys conducted in the summer and fall. Cyanotoxins will be measured by passing water through Solid Phase Adsorption Toxin Tracking (SPATT) samplers over a defined spatial domain and also by collecting water samples at specific sampling locations (~30 total over each mapping survey). The broad spatial coverage will help improve our understanding of relations between cyanotoxin production, transport, and drivers such as water temperature, nutrients, and light availability.

USGS boat-based mapping surveys cover approximately 350 miles of the Delta over 3 to 4 consecutive days. Underway flow-through sampling systems allow the simultaneous collection of in situ data for water quality, dissolved nutrients, and phytoplankton abundance. Like the fixed stations, phytoplankton taxonomic groups also will be assessed using a fluoroprobe that differentiates cyanobacteria, diatoms, green algae, and chlorophytes based on their characteristic pigments. The in situ high resolution measurements are supplemented with collection of discrete samples for determination of nitrate, ammonium, phosphorus, dissolved organic matter, microscopic enumeration of phytoplankton, and direct quantification of the picocyanobacterial abundances.

Relevance and Benefits

This research will contribute to USGS efforts nationwide to develop HAB and cyanotoxin monitoring approaches and initiates a much-needed HAB and cyanotoxin monitoring program for the Delta. The resulting data will assist local stakeholders in establishing practices for monitoring and management of cyanotoxin HABs. In addition, the boat-based approach will serve as a proof-of-concept for a new and novel method to collect highly resolved spatial water quality data alongside cyanotoxin concentration measurements that may be applied virtually anywhere cyanotoxin HABs occur.

The resulting data will permit insights into the locations and environmental conditions associated with HABs and cyanotoxin occurrence. This information also will support development of HABs forecasting models based on environmental conditions and the improvement of remote sensing algorithms for HABs detection. These data will provide, for the first time in the Delta, a multitude of environmental parameters alongside cyanotoxin analyses that can shed much-needed light on HAB development and cyanotoxin production in this complex system.