Harmful Algal Bloom (HAB) Cooperative Matching Funds Projects

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New projects from coast to coast will advance the research on harmful algal blooms (HABs) in lakes, reservoirs and rivers. The vivid emerald-colored algal blooms are caused by cyanobacteria, which can produce cyanotoxins that threaten human health and aquatic ecosystems and can cause major economic damage.

In Fiscal Years 2019 and 2020, Congress provided the USGS National Water Quality Program (NWQP) with additional resources to assess HABs. The NWQP is currently funding 16 projects in 12 geographic areas that advance real-time monitoring, remote sensing, and use of molecular techniques to identify and predict the occurrence of HABs and the toxins they produce. These new approaches will provide information that can act as an “early warning” of HABs, assist water-treatment plant operators in decision making, and build our knowledge of the cyanobacterial communities that cause HABs and the cyanotoxins produced.

Geographic areas with projects selected for funding

Continental US Map of USGS HABs Cooperarative Matching Funds Projects locations

HAB CMF Project Detail Map: California Bay Delta

California Bay-Delta—California

Contact: Angela HansenTamara Kraus

Mapping Cyanotoxin Concentrations in the Sacramento-San Joaquin Delta, California (funded in 2020).  This study will add cyanotoxin measurement to other water-quality data collected during boat-based mapping surveys. Cyanotoxins will be measured by passing water through SPATT (Solid Phase Adsorption Toxin Tracking) samplers and by collecting water samples to measure toxins at specific locations and times. 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. 

Fixed Station Cyanotoxins in the Sacremento-San Joaquin Delta (funded in 2020).  This study adds cyanotoxin measurements – using both SPATT (Solid Phase Adsorption Toxin Tracking) and whole water sampling approaches – to several monitoring stations in the Sacramento-San Joaquin Delta, a critical tidal aquatic habitat and drinking-water resource. These stations are equipped with sensors that measure flow, physico-chemical properties, nitrate, phytoplankton abundance and phytoplankton composition. The addition of cyanotoxin data to these stations will provide insight into drivers, sources, and transport of HABs and associated cyanotoxins.


HAB CMF Project Detail Map: New England


Cape Cod, Lake Champlain, and Central Maine—Vermont, Maine, and Massachusetts

ContactCharles W. Culbertson

Evaluating Environmental DNA Lake Assessments (funded in 2019). New molecular genetic techniques for sensitive detection of cyanobacteria will be applied to New England lakes and glacial kettle ponds on Cape Cod. Time-series analysis will be used to identify conditions leading to HAB development, including changes in the microbial community structure, and the time involved. The outcome of this project will provide resource managers and stakeholders a robust tool for the early detection of cyanobacteria associated with HAB formation and the presence of genes responsible for cyanotoxin production.






HAB CMF Project Detail Map: Delaware

Delaware River and Chesapeake Bay Basins—Maryland, Delaware, and Washington D.C.

ContactMark Nardi

Application of Landsat Data to Map Cyanobacteria Blooms in the Delaware River Basin (funded in 2019). This project will map the occurrence and distribution of cyanobacteria blooms starting in 2000 to present in the Delaware River Basin, providing a detailed picture of HAB occurrence in time and space. The mapping will be based on existing Landsat (satellite) data and in-situ water samples, and the resulting digital maps can be used by predictive models as input or for calibration and validation.








HAB CMF Project Detail Map: Idaho

Idaho Water Bodies—Idaho

Contact: Tyler King

Sentinel-2 and Landsat-8 algal indices delivery system for Idaho (funded in 2019). This project aims to provide water-resource managers with high-spatial resolution data suitable for detecting algal blooms in the large rivers and small and mid-sized lakes throughout Idaho. The data, from high-resolution Sentinel-2 and Landsat 8 satellite images, will include algal and chlorophyll-a detection indices suitable for operational use. The high-resolution images will enable detection of potential HABs occurrence for many new water bodies and will add greater detail to identification of spatial occurrence of blooms in larger lakes.








Inset map highlighting Kansas

Kansas Water Bodies—Kansas

Contact: Brian Kelly

Field verification of Cyanobacteria Assessment Network (CyAN) satellite products to estimate nearshore toxic cyanobacteria bloom accumulation in Kansas lakes and reservoirs (funded in 2020).  This study will collect critical field data from HAB-impacted reservoirs to validate satellite algorithms and metrics for detecting and quantifying potentially toxic HABs. The validation will improve the use of CyAN as a nationwide early-warning indicator for HABs and algal toxins in freshwater. The study will collect hydrologic, water-quality, biologic, meteorologic, hyperspectral data during satellite overflights to verify satellite data from HAB-impacted reservoirs, and implement uniform methodology for using innovative technology.






Inset map highlighting Michigan

Michigan Water Bodies - Michigan

Contact: Amanda Bell

Ramping up realtime HABs Monitoring in Michigan (funded in 2019).  The State of Michigan has selected key waterbodies for investigation of harmful algal blooms (HABs). For this study, USGS will work with Michigan Department of Environment, Great Lakes, and Energy (EGLE) to enhance current monitoring with additional sampling and incorporation of real-time sensor and satellite technologies. The objectives are to validate remote sensing data from the Cyanobacteria Assessment Network (CyAN) application and to use real-time sensor data to advance capabilities for HAB prediction. 







HAB CMF Project Detail Map: Finger Lakes

New York Finger Lakes—New York

ContactGuy M. Foster, Jennifer Graham

Finger Lakes Project Website

Imaging Flow Cytometry for Rapid Identification and Quantification of Cyanobacteria (funded in 2020).  Cyanobacterial identification and enumeration are essential to understanding bloom dynamics but can be costly and slow, sometimes requiring weeks or months for results. Laboratory-based imaging flow cytometry has the potential to reduce sample costs and provide results within 24 hours, but method validation is needed. In this study, imaging flow cytometry will be compared with traditional microscopy and field fluorometry and the advantages and disadvantages of each approach will be evaluated. 

Cyanobacterial Dynamics at the Sediment-Water Interface (funded in 2020).   Internal wave dynamics and interactions at the sediment-water interface may be an important driver of cyanobacterial bloom dynamics in the Finger Lakes, but connections between these processes are insufficiently understood. This study will assess and compare cyanobacteria and cyanotoxin genetic signatures and activity in bottom water and bed sediments, assess viability of cyanobacteria in sediments, and determine if resuspension by internal waves or fall turnover affects cyanobacteria in bottom waters and at the sediment-water interface.

Cyanobacterial Community Structure and Function in the Finger Lakes (funded in 2019). Genetic analysis to characterize cyanobacterial community composition (“who is there”) and function (“what are they doing”) will be added to advanced sensor technology and discrete water-quality data being used in Owasco and Seneca Lakes. The genetic analysis will add an important dimension to the ongoing advanced water-quality monitoring program designed to shed light on environmental conditions associated with bloom formation and cyanotoxin production.

Solid Phase Adsorption Toxin Tracking (SPATT) in the Finger Lakes (funded in 2019). SPATT samplers, which adsorb cyanotoxins in the water column for analysis,  are passive and time-integrative, capturing ephemeral toxin events that can be missed by traditional discrete sampling. In this project, SPATT samplers will be added to the advanced data-collection platforms on Owasco and Seneca Lakes.


HAB CMF Project Detail Map: Oregon

North Santiam and McKenzie River Basin reservoirs—Oregon

ContactKurt Carpenter   

Enhanced Monitoring of Harmful Algal Blooms—New Tools to Inform Dam Operations and Drinking Water Treatment (funded in 2019). This project will provide dam operators with real-time data on total chlorophyll, phycocyanin, and other HAB indicators, and a web-based profile analysis tool to understand HAB dynamics in Detroit Lake (North Santiam River Basin) and Cougar Reservoir (McKenzie River Basin). The information will identify the location of cyanobacteria in the water column, allow dam operators to tailor releases to minimize impacts from HABs, and provide drinking-water treatment plant operators with advance notice of cyanobacteria in raw water supplies.






Inset map highlighting Raritan area of New Jersey

Raritan River Basin—New Jersey

Contact: Pamela Reilly

Downstream Fate and Transport of Cyanobacteria and Cyanotoxins in the Raritan River Basin, New Jersey (funded in 2020).   This study evaluates the downstream fate and transport of cyanobacteria and cyanotoxins from headwater lakes  and reservoirs to drinking water intakes within the Raritan River Water Supply Complex. A combination of passive samplers, periodic water-quality samples, and continuous monitoring will be used to investigate effects of rapid changes in water-quality conditions on cyanotoxin production and transport. The data collected will serve as a baseline from which any future regulatory or mitigation actions to improve water quality can be measured. 







HAB CMF Project Detail Map: Tappan Lake

Tappan Lake—Ohio

ContactDonna Francy   

Models for Estimating Microcystin Concentrations in Source Waters at the Cadiz Water Treatment Plant (funded in 2019). For this study, the relations between phycocyanin and chlorophyll—pigments associated with cyanobacteria—and environmental data will be used in a quantitative model to aid in choosing among water-treatment options. The study will focus on continuous and discrete data collected at the intake to a water-treatment plant from Tappan Lake, and builds on an existing collaboration with the Cadiz Water Treatment Plant and the Muskingum Watershed Conservancy District.








HAB CMF Project Detail Map: Trinity, Sabine, and Red River

Texas Water Bodies—Texas

ContactChristopher Churchill   

Development of Near Real-Time Satellite Monitoring of HABs and CyanoHABs in Inland Water Bodies (funded in 2019). Remote sensing by satellites is a promising method for real-time detection of cyanobacteria over large areas, and this project will use field data from the Trinity, Sabine, and Red River Basins, among other water bodies throughout Texas, to adapt, enhance, and validate remote-sensing methods using high performance geoprocessing. A web-based application will be developed that allows users to identify—and possibly quantify—HABs.








HAB CMF Project Detail Map: Upper Midwest

Upper Midwest—Select river basins in Minnesota, Wisconsin, and North Dakota

ContactVictoria Christensen   

Beyond Microcystin (funded in 2019). Many cyanotoxins other than microcystin are present in HABs—this study will use solid phase adsorption toxin tracking (SPATT) technology and phycocyanin sensors within and outside areas such as Voyageurs National Park, Pipestone National Monument, and St. Croix Scenic Riverway to detect as many as 32 cyanotoxins. The results will shed light on the effect of differences in geography and setting on cyanobacteria and toxin production.