Harmful Algal Bloom (HAB) Cooperative Matching Funds Projects

Science Center Objects

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 through 2021, Congress provided the USGS National Water Quality Program (NWQP) with additional resources to assess HABs. The NWQP is currently funding 24 projects in 15 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.  All projects are conducted jointly with state, regional, tribal, and (or) local partners.

Geographic areas with projects selected for funding

Continental US Map of USGS HABs Cooperative Matching Funds Projects locations


California Bay-Delta—California

HAB CMF Project Detail Map: California Bay Delta

Managing HABs in California's Delta: Real-time Detection using Newly Developed Sensors (funded in 2021).
Contact: Brian Bergamaschi
This study will develop new sensors to measure cyanobacterial bloom density for real-time harmful algal bloom (HAB) assessments. The underwater sensors will calculate bloom density using optical image analysis and cyanobacterial spectral signatures. An “internet of things” data processing pipeline will be developed that can assimilate data from sensors, apply calculations, and transmit a compact data stream of results. These sensors will improve the suite of in situ tools that can be used to track changing HAB conditions in the Sacramento-San Joaquin Delta.

Mapping Cyanotoxin Concentrations in the Sacramento-San Joaquin Delta, California (funded in 2020).
Contact: Angela HansenTamara Kraus  
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 Sacramento-San Joaquin Delta (funded in 2020).
Contact: Angela HansenTamara Kraus
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.


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

HAB CMF Project Detail Map: New England

Evaluating Environmental DNA Lake Assessments (funded in 2019). 
Charles W. Culbertson
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.








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

HAB CMF Project Detail Map: Delaware

Application of Landsat Data to Map Cyanobacterial Blooms in the Delaware River Basin (funded in 2019). 
Mark Nardi
This project will map the occurrence and distribution of cyanobacterial blooms from 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.








Finger Lakes, Adirondack Lakes, and Lower Hudson River—New York

HAB CMF Project Detail Map: Finger Lakes, Adirondack Lakes, and Lower Hudson River

Finger Lakes Project Website

Cyanobacterial Occurrence and Bloom Development in Oligotrophic Adirondack Lakes (funded in 2021).
Contact: Jennifer Graham
Some of the most pristine lakes in New York experience cyanobacterial blooms. Once these lakes experience blooms, they appear more likely to experience them again. Blooms may restructure algal community composition and create bottom sediment “seed” banks that act as source areas for future bloom development. This study will characterize algal communities and potential seed bank source areas in oligotrophic lakes in northeastern New York, including the Adirondacks, that have and have not had documented blooms.

Cyanobacterial Transport and Community Dynamics in the Lower Hudson River (funded in 2021).
Contact: Jennifer Graham
The first documented cyanobacterial bloom on the Lower Hudson River occurred during summer 2019, but cyanobacterial dynamics are not well understood. This study will describe the spatial and temporal variability of cyanobacteria along the entire 137-mile reach of the Lower Hudson River and characterize the environmental factors associated with observed spatial and temporal gradients. In addition, this study will lay the groundwork for development of potential early indicators using the Hudson River Environmental Conditions Observing System (HRECOS).

Imaging Flow Cytometry for Rapid Identification and Quantification of Cyanobacteria (funded in 2020).
Guy M. Foster, Jennifer Graham
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).   
ContactGuy M. Foster, Jennifer Graham
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).
ContactGuy M. Foster, Jennifer Graham
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).
ContactGuy M. Foster, Jennifer Graham
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.


Idaho Water Bodies—Idaho

HAB CMF Project Detail Map: Idaho

Sentinel-2 and Landsat-8 Algal Indices Delivery System for Idaho (funded in 2019).
: Tyler King
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.







Kansas Water Bodies—Kansas

Inset map highlighting Kansas

Cyanobacteria Bloom Initiation in Slow Moving Streams (funded in 2021).
Brian Kelly
HAB development in slow-moving streams, wetlands, and oxbows and their relation to blooms in downstream reservoirs and rivers is largely unknown. This study will measure the hydrologic, water-quality, sediment, biological, meteorological, temporal, and spatial relations of HABs in headwater areas above Milford and Perry Lakes and the floodplain of the lower Kansas River, to receiving reservoirs or rivers. Study results will be used to help manage HABs and to better understand HAB occurrence in Kansas.

Field Verification of Cyanobacteria Assessment Network (CyAN) Satellite Products to Estimate Nearshore Toxic Cyanobacteria Bloom Accumulation in Kansas Lakes and Reservoirs (funded in 2020).  
Brian Kelly
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, and hyperspectral data during satellite overflights to verify satellite data from HAB-impacted reservoirs, and implement uniform methodology for using innovative technology.


Lake Superior Watersheds—Minnesota

Inset map highlighting Lake Superior and surrounding states

Making the Watershed Connection:  The Influence of Cyanobacteria, Sediment, Nutrient Loading, and Hydrology on Cyanobacterial Bloom Initiation in the Nearshore Environment (funded in 2021).
ContactCarrie Givens
Current management goals aim to address lake eutrophication and HABs by reducing watershed nitrogen and phosphorus inputs.  However, these goals do not account for watershed cyanobacteria inputs as a potential contributor to HABs and whether hydrologic event-based pulses of cyanobacteria may be an additional driver of bloom initiation. This study aims to make the connection between the land and lake by (1) assessing cyanobacteria growth and community indicators across riverine flow regimes, (2) determining spatial and temporal variation in nutrients, sediment, and cyanobacteria community throughout the watershed to nearshore, and (3) comparing the timing of nutrient and sediment loading to the nearshore with algal bloom initiation.




Michigan Water Bodies—Michigan

Inset map highlighting Michigan

Ramping up Realtime HABs Monitoring in Michigan (funded in 2020).
Amanda Bell
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. 








North Santiam and McKenzie River Basin reservoirs—Oregon

HAB CMF Project Detail Map: Oregon

Enhanced Monitoring of Harmful Algal Blooms—New Tools to Inform Dam Operations and Drinking Water Treatment (funded in 2019).
Kurt Carpenter
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.







Ohio River—Ohio and Kentucky

Detail map of the Ohio River project area

Ohio River Harmful Algal Blooms Early Warning System Expansion--Phase 2 Sites (funded in 2021).
Angie Crain
This project is an expansion to the scope of the FY20 phase 1 HAB monitoring strategies in the Ohio River Basin. The expansion project includes three additional sampling sites (two additional drinking water intake sites and the Ohio River at Pike Island, WV site) to compile sufficient data for predictive HAB model development at the five phase 1 sites.

Building a Harmful Algal Bloom Early Warning System in the Ohio River Basin (funded in 2020).
Angie Crain
This study will initiate harmful algal bloom (HAB) monitoring strategies for the Lower Ohio River Basin by quantifying and determining associations between cyanotoxins, cyanobacterial genes, nutrient concentrations, and continuous near-real-time water-quality measurements. The study also will identify cyanobacteria responsible for cyanotoxin production. Monitoring strategies will be the first step towards developing a system for estimating toxin concentrations in near-real-time using predictive models.


Ohio Water Bodies—Ohio

HAB CMF Project Detail Map: Ohio waterbodies

Cyanobacteria Assessment Network (CyAN)
Buck Creek CyAN (funded in 2021).
Caesar Creek CyAN (funded in 2020).
Jessica Cicale
Currently, limited scientific understanding of cyanobacterial harmful algal blooms (HABS) prevents prediction of toxic blooms in lakes of the United States. The CyAN is a multi-agency project between EPA, NASA, NOAA, and USGS to develop an early warning system using satellite data to detect cHABs in freshwater systems. The USGS began work at Caesar Creek Lake, Ohio as part of CyAN and will expand to a second lake, Buck Creek Lake, Ohio. This study will provide field data needed for ground-to-space validation of satellite algorithms and site-specific statistical models for prediction of potentially toxic HABs at lakes in the U.S. mid-continent region.  


Models for Estimating Microcystin Concentrations in Source Waters at the Cadiz Water Treatment Plant (funded in 2019). 
Donna Francy
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.


Raritan River Basin—New Jersey

Inset map highlighting Raritan area of New Jersey

Downstream Fate and Transport of Cyanobacteria and Cyanotoxins in the Raritan River Basin, New Jersey (funded in 2020). 
Contact: Pamela Reilly  
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 to measure any future regulatory or mitigation actions to improve water quality. 







Texas Water Bodies—Texas

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

Development of Near Real-Time Satellite Monitoring of HABs in Inland Water Bodies (funded in 2019).
Christopher Churchill   
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.








Upper Illinois River—Illinois

Detail map of the Illinois project area

Hydrodynamic and Temperature Model Investigation of Illinois River HABs (funded in 2021).
ContactPaul Rydlund
The purpose of this study is to develop a hydrodynamic and temperature model of a 20-mile reach of the upper Illinois River known to experience harmful algal blooms (HABs). The model will be two-dimensional in the vertical and longitudinal directions. Real-time flow and temperature data will be used to help develop and calibrate the model. Water balance, hydrodynamics, and temperature will be calibrated sequentially. Model results will indicate the role of hydrodynamics and temperature in HABs formation between Seneca, IL, and Starved Rock State Park







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

HAB CMF Project Detail Map: Upper Midwest

Beyond Microcystin (funded in 2019).
Victoria Christensen    
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 wilderness 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.