Cyanobacterial Harmful Algal Blooms (CyanoHABs)

Photo of Algal bloom at Grand Lake St. Mary’s, Ohio
Algal bloom at Grand Lake St. Mary's, Ohio, 2010. Photo by Russ Gibson, Ohio EPA

Algae are natural components of marine and fresh water flora performing many roles that are vital for the health of ecosystems. However, excessive growth of algae becomes a nuisance to users of water bodies for recreation activities and to drinking water providers. Excessively dense algal growth could alter the quantity and quality of light in the water column. Some types of algae may also cause harm through the release of toxins. When conditions like light availability, warm weather, low turbulence and high nutrient levels are favorable, algae can rapidly multiply causing "blooms." When blooms (or dense surface scums) are formed, the risk of toxin contamination of surface waters increases especially for some species of algae with the ability to produce toxins and other noxious chemicals. These are known as harmful algal blooms (HABs).

The Harmful Algal Bloom and Hypoxia Amendments Act of 2004 mandates that the National Oceanic and Atmospheric Administration (NOAA) advance the scientific understanding and ability to detect, monitor, assess, and predict HABs and hypoxia events in coastal waters and the Great Lakes. Research and advances in knowledge have occurred regarding marine HABs. However, research on U.S. inland and fresh waters HABs has not been as extensive with the greatest federal efforts focused on the Great Lakes.

HABs include different types of algal taxa such as dinoflagellates and diatoms, and cyanobacteria.  Bacteria, known as cyanobacteria or blue-green algae,  are of special concern because of their potential impacts on drinking and recreational waters. In freshwaters, cyanobacteria can produce unsightly conditions along the shoreline and in open waters degrading aquatic habitats and posing a health risk to humans, pets or wildlife. Increasingly, water managers and the public have expressed concerns about public health and environmental quality from HABs toxins in recreational and drinking waters have become an increasingly serious public health and environmental concern in the United States. EPA has compiled information on freshwater HABs and their effects to help inform the public about potential impacts of toxic algal blooms in freshwater.

Use the navigation quick tabs below to learn more about what causes cyanobacterial toxins, how to prevent, detect, mitigate and treat for them; the health and ecological effects of cyanotoxins; current research activities in the U.S.; and policies and regulations for cyanotoxins at the state and international levels.


Photo of Microcystis bloom at Ohio River, 2008. Photo by Jim Crawford, Ohio EPA
Microcystis bloom at Ohio River, 2008. Photo by Jim Crawford, Ohio EPA

The most commonly occurring groups of freshwater algae are diatoms, green algae, and blue-green algae (more correctly known as cyanobacteria). Cyanobacteria refer to a group of bacteria that possess characteristics of algae (chlorophyll-a and oxygenic photosynthesis). They are found in fresh, estuarine, and marine waters in the U.S. Cyanobacteria are often confused with filamentous green algae, because both can produce dense mats that can impede activities like swimming and fishing, and may cause odor problems and oxygen depletion. However, unlike cyanobacteria, filamentous algae are not generally thought to produce toxins. Freshwater cyanobacterial blooms that produce highly potent cyanotoxins are known as cyanobacterial HABs (cyanoHABs). These species are capable of producing compounds that are hepatotoxic (affect the liver), neurotoxic (affect the nervous system) and acutely dermatotoxic (affect the skin). Hepatotoxic freshwater blooms of cyanobacteria are more commonly found than neurotoxic blooms throughout the world.

Photo of Anabaena bloom on Lake Pontchartrain, Louisiana, 1997. Photo by John Burns
Anabaena bloom on Lake Pontchartrain, Louisiana, 1997. Photo by John Burns

Freshwater cyanobacterial blooms may be dominated by a single-species or be composed of a variety of toxic and non-toxic strains (i.e., a specific genetic subgroup within a particular species). Cyanotoxins are produced and contained within the actively growing cyanobacterial cells (i.e., intracellular toxins). The release of these toxins into the surrounding water, as dissolved (extracellular) toxins, occurs mostly during cell death and lysis (i.e., cell rupture) of a cyanobacterial bloom, rather than by continuous excretion from the cells.

Cyanotoxins can be produced by a wide variety of planktonic (i.e., free living in the water column) cyanobacteria. Some of the most commonly occurring genera are Microcystis, Anabaena, and Planktothrix (Oscillatoria).

Photo of Planktothrix bloom at Grand Lake St. Mary, Ohio. Courtesy of Keith Loftin, USGS
Planktothrix bloom at Grand Lake St. Mary, Ohio. Courtesy of Keith Loftin, USGS

Microcystis is the most common bloom-forming genus, and is almost always toxic. Microcystis blooms are a greenish, thick, paint-like (sometimes granular) material that accumulates along shores. Scums that dry on the shores of lakes may contain high concentrations of microcystin for several months, allowing toxins to dissolve in the water even when the cells are no longer alive or after a recently collapsed bloom.

Species of the filamentous genus Anabaena form slimy summer blooms on the surface of eutrophic lakes and reservoirs. Anabaena blooms may develop quickly. They may look like green paint. In less eutrophic waters, some species also form colonies, which are seen as large dark dots in water samples and on filters after filtration.

Photo of Nostoc dominated bloom
Nostoc dominated bloom. Courtesy of J. Hyde, NYS DOH

Planktothrix agardhii (previously named Oscillatoria agardhii) forms long, slender, straight filaments that usually remain separate but form dense surface scums. Its presence may be revealed by a strong earthy odor and the filaments are easily detected visually in a water sample.

Based on the surveys that have been carried out to date in U.S. waters, the most commonly identified cyanotoxins are microcystins, cylindrospermopsins, anatoxins and saxitoxins.


Photo of Woronichinia-Microcystis bloom
Woronichinia-Microcystis bloom. Courtesy of Keith Loftin, USGS

Microcystins are a group of at least 80 toxin variants which share a cyclic heptapeptide structure and primarily affect the liver (hepatotoxin). Microcystins are the most widespread cyanobacterial toxins and can bioaccumulate in common aquatic vertebrates and invertebrates such as fish, mussels, and zooplankton. Microcystins are produced by Microcystis, Anabaena, Planktothrix (Oscillatoria), Nostoc, Hapalosiphon, Anabaenopsis and Snowella lacustris. Nodularin, which is structurally related to microcystin and has a similar mode of toxicity, has been isolated from only one species of cyanobacteria, Nodularia spumigena. Recent evaluation of carcinogenesis from microcystin exposure by the International Agency for Research in Cancer has determined that microcystin- LR is possibly carcinogenic to humans (Group 2B), and has been linked to incidences of human liver and colon cancer.


Photo of Aphanizomenon flosaquae dominated bloom
Aphanizomenon flosaquae dominated bloom. Courtesy of Keith Loftin. USGS

Cylindrospermopsin is usually produced by Cylindrospermopsis raciborski, Aphanizomenon ovalisporum, Anabaena bergii, Umezakia natans, and Raphidiopsis curvata. The primary toxic effect of this toxin is irreversible damage to the liver. It also appears to have a progressive effect on several other vital organs. Effects of poisoning in humans included hepatoenteritis and renal insufficiency. Although the evidence of carcinogenicity in humans and experimental animals is inadequate, there is strong evidence of the tumour-promotion capacity of microcystin-LR to place them in Group 2B as possibly carcinogenic to humans.

Anatoxins binds to neuronal nicotinic acetylcholine receptors affecting the central nervous system (neurotoxins). There are multiple variants, including anatoxin-a, homoanatoxin-a, and anatoxin-a(s). These toxins are mainly associated with the cyanobacterial genera Oscillatoria species, Cylindrosperum, Planktothrix spp., Aphanizomenon spp., Lyngbya and species such as Anabaena flos–aquae and A. planktonica.

Saxitoxins are representative of a large toxin family referred to as the Paralytic Shellfish Poisoning (PSP) toxins. When toxigenic marine dinoflagellates are consumed by shellfish, toxins concentrate and toxic quantities are delivered to consumers of the shellfish. These toxins have been reported also in freshwater cyanobacteria including Aphanizomenon flos–aquae, Anabaena circinalis, Lyngbya wollei, Planktothrix spp. and a Brazilian isolate of C. raciborskii.

Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms
US EPA IRIS Toxicological Reviews for Microcystins, Anatoxin-a, and Cylindrospermopsin
WHO Water Related Diseases: Cyanobacterial Toxins
WHO Cyanobacteria and Cyanotoxins in Drinking Water
WHO IARC Monographs on the Evaluation of Carcinogenic Risks to Humans; Ingested Nitrate and Nitrite, and Cyanobacterial Peptide Toxins, VOLUME 94
CDC Harmful Algal Blooms (HABs)
CDC Recent Water-related Response Activities

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.


To determine the occurrence and risk of cyanoHABs, it is important to collect samples that reflect the actual site or source conditions. Samples may consist of water, plankton, invertebrates, vertebrates, or sediments. Although chlorophyll–a and cyanobacterial cells have been used as a first estimation of maximum intracellular microcystin concentration, it is important to isolate a pure culture of the strain and characterize and quantify the toxin to confirm that a particular cyanobacterial strain is the source of the toxin.

There is a diverse range of rapid screen tests and laboratory methods used to detect and identify cyanotoxins in water and cyanobacteria cells (see table below provided by Keith Loftin, USGS). These methods can vary greatly in their degree of sophistication and the information they provide.

Often, more than one toxin may be present in a sample, therefore, a single method will not suffice for the identification and accurate quantification of many cyanotoxins. This laboratory analysis can be expensive and time consuming, and often requires lengthy sample processing to concentrate the toxins and eliminate matrix contaminants. In addition, the ability of these techniques to identify the toxins is restricted by the lack of standard reference materials for the toxins and readily available, validated, analytical methods that are capable of detecting the range of cyanotoxins known to exist.

Analysis of microcystins is most commonly carried out using reversed-phase high performance liquid chromatographic methods (HPLC) combined with ultra-violet (UV) detection. Analytical methods such as enzyme–linked immunosorbent assays (ELISA) already exist to analyze cyanobacterial hepatotoxins and saxitoxins, and the protein phosphatase inhibition assay (PPIA) can be used for microcystins. These two methods are sensitive, rapid, and suitable for large-scale screening but are predisposed to false positives and unable to differentiate between toxin variants. The liquid chromatography/mass spectrometry (LC/MS) method can be fast in identifying the toxicants in the samples. Conventional polymerase chain reaction (PCR), quantitative real–time PCR (qPCR) and microarrays/DNA chips can be used to detect microcystin/nodularin and saxitoxin producers. However, relatively little work has been done on methods for detection of other toxins, including anatoxins and cylindrospermopsins. Saxitoxins are the exception, as they also occur widely in the marine environment and many methods have been developed for their detection in shellfish.

The following table describes the methods available for cyanotoxin measurement in freshwater. The information in the table is adapted from a presentation entitled Analytical Methods for Cyanotoxin Detection and Impacts on Data Interpretation by Keith Loftin, Jennifer Graham, Barry Rosen (U.S. Geological Survey) and Ann St. Amand (Phycotech). The presentation was given on April 26, 2010 at the 2010 National Water Quality Monitoring Conference at Denver, CO.

Methods Available for Cyanotoxin Detection

 Freshwater Cyanotoxins
   Anatoxins  Cylindrospermopsins  Microcystins  Nodularins  Saxitoxins
 Biological Assays (Class Specific Methods at Best)
 Mouse  Yes  Yes  Yes  Yes  Yes
 PPIA  No  No  Yes  No  No
 Neurochemical  Yes  No  No  No  Yes
 ELISA  In progress  Yes  Yes  Yes  Yes
 Chromatographic Methods (Compound Specific Methods)
 Gas Chromatography
 GC/FID  Yes  No  No  No  No
 GC/MS  Yes  No  No  No  No
 Liquid Chromatography
 LC/UV (or HPLC)  Yes  Yes  Yes  Yes  Yes
 LC/FL  Yes  No  No  No  Yes
 Liquid Chromatography combined with mass spectrometry
 LC/IT MS  Yes  Yes  Yes  Yes  Yes
 LC/TOF MS  Yes  Yes  Yes  Yes  Yes
 LC/MS  Yes  Yes  Yes  Yes  Yes
 LC/MS/MS  Yes  Yes  Yes  Yes  Yes

Acronyms in the table:

ELISA: Enzyme-Linked Immunosorbent Assays
PPIA: Protein Phosphatase Inhibition Assays
GC/FID: Gas Chromatography with Flame Ionization Detection
GC/MS: Gas Chromatography with Mass Spectrometry
HPLC or LC/UV: Liquid Chromatography / Ultraviolet-Visible Detection
LC/FL: Liquid Chromatography/Fluorescence

LC/IT MS: Liquid Chromatography Ion Trap Mass Spectrometry
LC/TOF MS: Liquid Chromatography Time-of-Flight Mass Spectrometry
LC/MS: Liquid Chromatography Single Quadrupole Mass Spectrometry
LC/MS/MS: Liquid Chromatography Triple Quadrupole Mass Spectrometry

You will need Adobe Reader to view some of the files on this page. See EPA’s About PDF page to learn more.

US EPA Environmental Technology Verification Program, Immunoassay Test for Microcystins
Nova Scotia Department of the Environment, Evaluation of Two Test Kits for Measurement of Microcystin Concentrations (PDF) (19 pp, 6MB) 
Presentations EPA Workshop on Cyanobacteria and Cyanotoxins Occurrence and Detection Methods, July 2012 (PDF) (24 pp, 34MB) 
Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms
USGS Guidelines for Design and Sampling for Cyanobacterial Toxin and Taste-and-Odor Studies in Lakes and Reservoirs
Monitoring and Event Response for Harmful Algal Blooms in the Lower Great Lakes (MERHAB-LGL) Analytical Techniques Webpage
WHO Toxic cyanobacteria in water: A guide to their public health consequences, monitoring and management
WHO Guidelines for Safe Recreational Waters Volume 1 - Coastal and Fresh Waters
Australia Guidelines for Managing Risks in Recreational Water 
Microcystins ELISA Test Kits Health Canada Algal Toxin Tests Kits Report (PDF) (21 pp, 142K)
Indiana Department of Environmental Management, Blue-Green Algae Sampling Resource List (PDF) (2 pp, 184K)

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.


Blooms of cyanobacteria in the United States have been associated with the death of wildlife and domestic animals. They may pose a risk to human health through exposure to contaminated recreational or drinking water, and fish and shellfish consumption.

The most common exposures to cyanobacteria and their toxins are believed to occur during recreational activities via the oral, dermal, and inhalation routes. Oral exposure may occur from accidental or deliberate ingestion of recreational water. Dermal exposure may occur by direct contact of exposed parts of the body to water containing cells, or inhalation may occur through the aspiration of water containing cyanobacteria cells and their toxins. Wind-driven currents may cause buoyant cyanobacterial blooms to amass on shorelines. These accumulations contain orders of magnitude more cyanobacterial cells than blooms in open waters, thus presenting more of a health risk to humans and animals. Cyanobacterial cells can also accumulate in bathing suits, particularly diving suits. When the algal cells break the wearer's skin is exposed to the toxins.

Other major routes of human exposure are through ingestion of cyanotoxin-contaminated drinking water, inhalation while showering, dietary intake via consumption of cyanotoxins in contaminated foods and algal dietary supplements, and exposure from water used in medical treatments (e.g., medical dialysis). The consumption of fish flesh (muscle) is usually considered safe but there are fish species and fish organs, especially the liver, and stomach/intestinal contents which may contain considerable amounts of cyanotoxins. Consumption of mussels and clams collected during cyanobacterial blooms or immediately after blooms should be avoided. Generally, hepatotoxic microcystins and nodularins are more common than the neurotoxins in aquatic animals including mussels, clams, crab larvae, prawns, crayfish and zooplankton, causing hepatotoxic effects in the fish and the accumulation of toxins in their organs. Consumption of contaminated shellfish and fish with cyanotoxins can lead to impacts on the liver and the nervous system.

Adverse health outcomes from exposure to cyanotoxins may range from a mild skin rash to serious illness or death. Acute illnesses caused by exposure to cyanotoxins have been reported. Symptoms range from allergic–like reactions (e.g., rhinitis, asthma, eczema, and conjunctivitis) to flu–like reactions (skin rashes, gastroenteritis, and respiratory irritation). Allergic or irritative dermal reactions of varying severity have been reported from recreational exposures to several freshwater cyanobacterial genera such as Anabaena, Aphanizomenon, Nodularia, and Oscillatoria. Endotoxins, the blue–green pigment of the cyanotoxins (phycocyanin) and dermal toxins produced by Lyngbya and Planktothrix species have been linked to skin and eye irritation from exposure during swimming.

In addition, microcystin, anatoxin-a and saxitoxin, have been linked to gastrointestinal illness, liver disease, neurological effects, skin reactions, and possible cancer in humans. Experimental studies have demonstrated the tumor promotion activity of microcystins and nodularin and the potential for cancer (tumor) development by cylindrospermopsin. The most serious incidence occurred in 1996 at a hemodialysis clinic in Brazil when the deaths of over 50 patients receiving dialysis were attributed to exposure to microcystins which were later identified in the clinic’s water supply.

Cyanobacterial blooms may cause detrimental effects on aquatic ecosystems. High biomass blooms, whether of toxic or nontoxic species, can accumulate as thick scums and mats, which decompose causing excessive oxygen consumption (hypoxia), and lead to mortality and degradation of fish, shellfish, invertebrate, and plant habitats. The blooms may also affect benthic flora and fauna due to decreased light penetration. Toxic blooms from some cyanobacteria genera (e.g., Anabaena circinalis, Aphanizomenon flosaquae, Cylindrospermopsis raciborskii, and Microcystis aeruginosa) may lead to inhibition of other phytoplankton and suppression of zooplankton grazing, leading to reduced growth and reproductive rates and changes in community structure and composition.

In addition to the production of toxins, cyanobacteria have often been associated in drinking water with taste and odor problems. Algal scums can be quickly broken by wave action and redispersed by wind mixing. In shallow bays, scums may take a long time to disperse and cells may disintegrate and die. Dying and lysing cells release their contents (toxins) into the water and are subject to rapid putrefaction of the material. Blooms produce a variety of odor and taste compounds, such as geosmin and 2–methylisoborneol (MIB), which are not toxic but are a nuisance to the public. The cyanobacterial genera that are known to produce geosmin are Anabaena, Aphanizomenon, Lyngbya, Microcystis, Oscillatoria, Phormidium, Schizothrix and Symploca. However, taste and odor issues are complex and are not solely associated with the presence of cyanobacteria. Many actinomycetes bacteria such as Actinomyces and Streptomyces species, aquatic fungi and myxobacteria can also produce these compounds.

Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms
US EPA Harmful Algal Blooms and Seafood Safety
US EPA IRIS Toxicological Reviews for Microcystins, Anatoxin-a, and Cylindrospermopsin
WHO Cyanobacterial toxins: Microcystin-LR in Drinking-water
WHO Water Related Diseases: Cyanobacterial Toxins
Health Canada Blue-Green Algae (Cyanobacteria) and their Toxins
Presentations EPA Webinar Human Health Risks Associated with Cyanobacteria and Cyanotoxins Exposure, May 22, 2013
Presentations EPA Webinar Human Health Risks Associated with Cyanobacteria and Cyanotoxins Exposure, May 23, 2013

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.


In 1998, Congress passed the Harmful Algal Bloom and Hypoxia Research and Control Act (HABHRCA) to address cyanobacterial HABs that impacted living marine resources, fish and shellfish harvests and recreational and service industries along the U.S. coastal waters. In 2004, Congress reauthorized and expanded HABHRCA by passing the Harmful Algal Bloom and Hypoxia Amendments Act required federal agencies to assess HABs to include freshwater and estuarine environments and develop reports and plans to reduce the likelihood of HAB formation and to mitigate their damage.  On February 12, 2014, HABHRCA passed the U.S. Senate and passed to the U.S. House of Representatives for consideration.

In 2008, the report entitled Scientific Assessment of Freshwater Harmful Algal Blooms was generated to examine the causes, consequences, and economic costs of freshwater HABs and to establish priorities and guidelines for a research program on HABs in freshwater environments. This document is based, in large part, on the proceedings of the International Symposium on Cyanobacterial Harmful Algal Blooms (ISOC-HAB), a meeting convened by EPA and sponsored by a variety of Federal agencies, to describe current scientific knowledge and identify priorities for future research on cyanobacterial HABs. A detailed account of the research needs related to HABs listed at the Symposium may be found in

Below is a list of recent research activities supported by EPA’s Office of Research and Development:

Research activities and programs from EPA Regional Offices and Laboratories

Research from other Federal Agencies


For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.


Cyanobacteria have been present in aquatic ecosystems for a very long time, with their first occurrence dating back at least 2.7 billion years ago. They are generally present, but not necessarily dominant, in freshwater bodies in the U.S. However, there is widespread agreement within the scientific community that the incidence of cyanoHABs is increasing both in the U.S. and worldwide. This increase is attributed to increasing anthropogenic activities and their interaction with a suite of physical, chemical and biological factors such as competition and grazing. Some physical factors include the availability of light, meteorological conditions, alteration of water flow, vertical mixing and temperature. Chemical factors include pH changes, nutrient loading (principally in various forms of nitrogen and phosphorus) and trace metals.

As a result of the interplay of these factors, there may be large temporal fluctuations in the levels of cyanobacteria and their toxins in predominating species. The ratio of nitrogen to phosphorus, organic matter availability, temperature, and light attenuation among others, likely play an interactive role in determining corresponding HAB composition and toxin production. Fresh waters that are high in phosphorus but low in nitrogen are typically dominated by toxic nitrogen fixing genera (e.g., Anabaena, Aphanizomenon, Nodularia and Cylindrospermopsis). Such “biological nitrogen fixation” results in the production of ammonia, an important process in the global nitrogen cycle. On the other hand, surface waters that are high in nitrogen are dominated by toxic blooms of non-nitrogen fixing genera (Microcystis, Lyngbya, Planktothrix).

Historically, HABs have been strongly correlated with excessive levels of nutrients in waterbodies with low turbidity. Point sources (which may include discharges from sewage treatment plants and confined animal feeding operations) and non-point sources (which may include diffuse runoff from agricultural fields, roads and stormwater), may be high in nitrogen and phosphorus and can promote or cause excessive fertilization (eutrophication) of both flowing and non-flowing waters.

In addition, climatic changes, including variation in rainfall patterns, flood and drought frequencies, dust storms, tropical storms, and the intensity of hurricanes, have impacted nutrient cycling in freshwater bodies and may support cyanobacterial and algal communities and bloom development. The following conceptual figure illustrates the environmental processes that control cyanobacterial blooms, including man-made management actions and impacts of climate change.

Photo of Controlling harmful cyanobacterial blooms in a world experiencing anthropogenic and climatic-induced change
Source: Pearl, H., Hall, N., and Calandrino, E. (2011) Controlling harmful cyanobacterial blooms in a world experiencing anthropogenic and climatic-induced change. Science of the Total Environment, Vol. 409, Issue 10, April, 2011, Pages 1739-1745

Preventative measures are the preferred approach to managing the occurrence of cyanoHABs. The most effective preventative measures are those that seek to control the anthropogenic influences that promote blooms such as the leaching and runoff of excess nutrients. Management practices for nutrients, specifically nitrogen and phosphorus, should have the goal of reducing loadings from both point and nonpoint sources, including water treatment discharges, agricultural runoff, and stormwater runoff. Devices that result in the mixing of lakes (for example, by air bubbling), enhance vertical mixing of the phytoplankton, which minimizes the formation of surface blooms of buoyant cyanobacteria. Also, increasing the water flow through lakes or estuaries reduces water residence time and inhibits cyanobacteria blooms. However, these efforts can be expensive and are best suited to small affected water bodies.

Climate Change and Harmful Algal Blooms Fact Sheet
Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms
US EPA Climate Change Indicators in the United States
US EPA Watershed Framework Approach
US EPA Watershed Analysis and Management (WAM) Guide for States and Communities
US EPA OW Nutrient Pollution Video

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.


The control and management of cyanoblooms in surface water and treatment of cyanotoxins in drinking water is critical to protect human health. An effective but expensive management practice for small watersheds is the application of compounds to chemically-precipitate phosphorus, followed by removal of the sediment by dredging. Adding alum, ferric salts or clay products effectively settles the phosphorus to the sediment layer reducing concentrations and the potential for bloom formation. Suction dredging of the top half meter of sediments removes nutrients and prevents bloom formation. Repeated dredging at intervals of several years may be necessary to prevent the re-release of phosphorus. Monitoring phosphorus concentrations is recommended to evaluate if dredging is needed. Effective treatment requires careful design and understanding of the sediment chemistry and hydrology of the water to be treated.

Mitigation (or remedial) measures can be employed once blooms have already occurred to control the phytoplankton blooming rate and to remove blooms. Remedial measures include the physical removal of surface scums and the application of algaecides and other chemicals (e.g. copper sulfate and lime) to control blooms. The precipitation of algal blooms with lime does not appear to cause cell lysis and toxin release into the water. However, application rates are high and, therefore, are recommended only for small lakes. Treatment of algal blooms with copper sulfate leads to cell breaking and a substantial release of cyanotoxins into the water, greatly increasing the risk of toxin contamination and treatment costs. Copper may also be toxic to other aquatic wildlife in the lake. Algaecides also lead to cell breaking and should be applied when cell numbers are low to avoid excessive toxin contamination following rupture of the cells. Algaecides application in drinking water reservoirs may required monitoring since toxins released in water after cell breaking may be a problem and difficult to remove by conventional drinking water treatment processes.

Biological mitigation measures include different approaches to change the aquatic food web to increase grazing pressure on cyanobacteria by introducing of functionally competitive species (e.g., diatoms). Competition and grazing can affect the net growth rates of algae in water but the effectiveness in reducing harmful algae depends on the population density of the harmful algae and nutrients concentrations. In some cases, grazing may increase nutrient regeneration affecting the availability of some nutrient forms for the algae to consume. Although competition and grazing have been studied for a long time, there are still important gaps, in particular, understanding the grazing of phytoplankton with different nutritional status.

Cyanobacterial problems and cyanotoxins in water supplies may also be mitigated during drinking water treatment. Conventional water treatment (flocculation, coagulation, sedimentation and filtration) is effective in removing algal cells and intracellular cyanotoxins. Drinking water treatment facilities that use microstrainers or fine screens to remove debris from the water intake are useful in removing larger algae, cyanobacterial cells and aggregated cells. Oxidants are often added at the intake to reduce taste and odor problems and to discourage biological growth (zebra mussels, biofilm, and algae) on the intake pipe. However, pretreatment oxidation is not recommended because it may rupture cyanobacteria cells releasing the cyanotoxin to the water column. This may also cause the formation of chlorinated disinfection by-products.

When algae are blooming, a substantial proportion of toxins are expected to be released to the water column. Conventional water treatment is usually not effective in removing extracellular cyanotoxins (soluble toxins). Neither aeration nor air stripping are effective treatments for removing soluble toxins or cyanobacterial cells. Advanced treatment processes, such as powdered and granular activated carbon adsorption, must be implemented to remove extracellular toxins as well as intact cells.

Different cyanotoxins react differently to chlorination. While chlorination is an effective treatment for destroying microcystins and cylindrospermopsin, effectiveness is dependent on the pH. Anatoxin–a is not degraded by chlorination. Other chlorine disinfectants such as chloramines and chlorine dioxide that are frequently used to minimize the formation of regulated disinfection by-products, have little impact on microcystin, cylindrospermopsin, anatoxin-a, and saxitoxins. Therefore, those treatment utilities that use disinfectants other than chlorine in order to reduce the formation of disinfection by-products may not have an oxidant treatment barrier for cyanotoxin inactivation.

Other disinfection techniques like ozone and Ultraviolet (UV) light have been shown to be effective in inactivating cyanotoxins. Ozone is a good oxidant of microcystins, anatoxin-a and cylindrospermopsin. Saxitoxins, however, appear to have low to moderate susceptibility to ozone oxidation. Ultraviolet (UV) is an effective treatment in destroying microcystin, anatoxin-a, and cylindrospermopsin cells. However, it requires high dosages, making it a non-viable treatment barrier for cyanotoxins.

In summary, mitigation and treatment techniques that are applied once a bloom has formed can be important management tools, but preventing the bloom from forming is the better choice when it can be achieved. A wide range of technologies are available for treatment of drinking water sources contaminated with cyanotoxins. However, all the technologies have their own advantages and limitations. Choosing the most efficient, safest, and cost-effective approach should be done on case-by-case basis.

Minnesota Department of Health Microcystin-LR in Drinking Water Fact Sheet (PDF) (2 pp, 125 K)
Treatment Options, International Guidance Manual for the Management of Toxic Cyanobacteria, Water Quality Research Australia
Harmful Algal Blooms (HAB) – The Beach Manager's Manual (PDF) (8 pp, 3.4MB)
Cyanobacteria and Cyanotoxins: Information for Drinking Water Systems fact sheet (PDF) (9 pp, 78K) 
Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms
US EPA Watershed Framework Approach
US EPA Watershed Analysis and Management (WAM) Guide for States and Communities
WHO Toxic cyanobacteria in water: A guide to their public health consequences, monitoring and management
WHO Guidelines for Safe Recreational Waters Volume 1 - Coastal and Fresh Waters
Australia Guidelines for Managing Risks in Recreational Water
Management Strategies for Cyanobacteria (Blue-Green Algae) and their Toxins: a Guide for Water Utilities

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.


Currently there are no U.S. federal guidelines, water quality criteria and standards, or regulations concerning the management of harmful algal blooms in drinking water under the Safe Drinking Water Act (SDWA) or in ambient waters under the Clean Water Act (CWA). However, several countries outside the U.S. do have various values that serve as guidelines or thresholds for certain management actions.

The SDWA requires EPA to publish a list of unregulated contaminants that are known or expected to occur in public water systems in the U.S., with a frequency and at levels of public health concern and where there is a meaningful opportunity for health risk reduction. This list is known as the Contaminant Candidate List (CCL). EPA’s Office of Water has listed cyanobacteria and cyanotoxins on the three drinking water CCLs (CCL 1 of 1998, CCL 2 of 2005 and CCL 3 of 2009). Based on toxicological, epidemiology and occurrence studies, the EPA Office of Ground Water and Drinking Water has focused on 3 of the over 80 variants of cyanotoxins reported, recommending Microcystin congeners LR, YR, RR and LA, Anatoxin–a and Cylindrospermopsin for further research activities. The EPA uses the Unregulated Contaminant Monitoring Rule (UCMR) program to collect data for contaminants suspected to be present in drinking water that do not have health–based standards.

The absence of standardized analytical methods for individual toxins has prevented EPA from including cyanobacterial toxins in the UCMR. Due to this factor and to the absence of certified toxin standards to support analyses and the lack of capacity to deal with multiple toxin congeners, EPA has not made regulatory determinations or established any guidelines for cyanobacteria and their toxins in drinking water.

The World Health Organization (WHO) released in 1998 a provisional guideline of 1 μg/L for microcystin-LR in drinking-water. This guideline value covers only microcystin-LR since there are insufficient data to derive a guideline value for cyanobacterial toxins other than microcystin-LR. For recreational waters, the WHO considered a single guideline value for cyanobacteria or cyanotoxins to be not appropriate. Due to the variety of exposures in recreational activities (contact, ingestion and inhalation) it is necessary to differentiate between the chiefly irritative symptoms caused by unknown cyanobacterial substances and the more severe hazard of exposure to high concentrations of known cyanotoxins, particularly microcystins. The WHO guidance values for the relative probability of acute health effects during recreational exposure to cyanobacteria and microcystins are:

Relative Probability of Acute Health Effects Cyanobacteria (cells/mL) Microcystin-LR (µg/L) Chlorophyll-a (µg/L)
Low < 20,000 <10 <10
Moderate 20,000-100,000 10-20 10-50
High 100,000-10,000,000 20-2,000 50-5,000
Very High > 10,000,000 >2,000 >5,000

Several U.S. states have implemented standards or guidelines that apply to cyanotoxins and cyanobacteria in drinking water and recreational water using risk assessment methods and the guidelines provided by the WHO for recreational waters.  Guidance values for drinking water have been adopted by three states in the United States:

State Drinking Water Guidance/Action Level
Minnesota Microcystin-LR: 0.04 µg/L
Ohio Microcystin: 1 µg/L
Anatoxin-a: 20 µg/L
Cylindrospermopsin: 1 µg/L

Saxitoxin: 0.2 µg/L
Oregon Microcystin-LR: 1 µg/L
Anatoxin-a: 3 µg/L
Cylindrospermopsin: 1 µg/L

Saxitoxin: 3 µg/L

For a summary of the U.S. states with guidance values being used to post advisories and beach closures see the table below or see the Monitoring Recreational Freshwaters paper by Jennifer L. Graham, Keith A. Loftin, and Neil Kamman (2009).

State Recreational Water Guidance/Action Level Recommended Action
California Microcystin: 0.8 µg/L
Anatoxin-a: 90 µg/L
Cylindrospermopsin: 4 µg/L
Indiana Level 1: very low/no risk < 4 µg/L microcystin-LR
Level 2: low to moderate risk 4 to 20 µg/L microcystin-LR
Level 3: serious risk > 20 µg/L microcystin-LR
Warning Level: Cylindrospermopsin: 5 ppb
Level 1: use common sense practices
Level 2: reduce recreational contact with water
Level 3: consider avoiding contact with water until levels of toxin decrease
Iowa Microcystin ≥ 20 µg/L Caution - bloom present no toxin data available
Warning - when toxin levels exceed 20 µg/L
Kansas PHA: >4 µg/L to <20 µg/L for microcystin or > 20,000 cell/mL to <100,000 cell/mL cyanobacteria cell counts
PHW: > 20 µg/L or > 100,000 cell/mL cyanobacterial cell counts and visible scum present
Public Health Advisory (PHA): avoid contact
Public Health Warning (PHW): all contact with water is restricted
Massachusetts 14 µg/L for microcystin-LR and ≥ 70,000 cells/mL for cyanobacteria cell counts Advisory - Avoid contact with water
Nebraska Microcystin ≥ 20 µg/L Health Alert
New Hampshire >50% of cell counts from toxigenic cyanobacteria Public Health Advisory
North Carolina Visible discoloration of the water or a surface scum may be considered for microcystin testing Advisory/Closure
Ohio Microcystin-LR: PHA: 6 µg/L; NCA: 20 µg/L
Anatoxin-a: PHA: 80 µg/L; NCA: 300 µg/L
Saxitoxin: PHA: 0.8 µg/L; NCA: 3 µg/L
Cylindrospermopsin: PHA: 5 µg/L; NCA: 20 µg/L
Public Health Advisory (PHA) - swimming and wading are not recommended, water should not be swallowed and surface scum should be avoided.
No Contact Advisory (NCA) -recommend the public avoid all contact with the water
Oklahoma 100,000 cell/mL of cyanobacteria cell counts and > 20µg/L for microcystin Blue-Green Algae Awareness Level Advisory
Oregon Option 1: Visible scum and cell count or toxicity
Option 2: Toxigenic species >100,000 cells/mL
Option 3: Microcystis or Planktothrix > 40,000 cells/mL
Option 4: Toxin Testing Microcystin: 8µg/L Anatoxin-a: 20 µg/L Cylindrospermopsin: 6µg/L Saxitoxin: 100 µg/L
Public Health Advisory
Rhode Island Visible cyanobacteria scum or mat and/or cyanobacteria cell count > 70,000 cells/mL and/or ≥14 µg/L of microcystin-LR Health Advisories
Texas >100,000 cell/mL of cyanobacteria cell counts and >20µg/L microcystin Blue-Green Algae Awareness Level Advisory
Vermont 4,000 cells/mL cyanobacteria cell counts or ≥ 6µg/L microcystin-LR and the visible presence of cyanobacterial scum
Anatoxin-a ≥ 10 µg/L
Beach Closure
Virginia Microcystin provisional action level: 6µg/L Advisory/Closure
Washington Microcystin-LR: 6 µg/L
Anatoxin-a: 1 µg/L
Cylindrospermopsin: 4.5 µg/L
Saxitoxin: 75 µg/L
Tier 1. Caution: when a bloom is forming or a bloom scum is visible (toxic algae may be present)
Tier 2. Warning: Toxic algae present
Tier 3. Danger: Lake closed
Wisconsin > 100,000 cells/mL or scum layer Advisory/Closure

Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms
US EPA Contaminant Candidate List (CCL) and Regulatory Determinations
US EPA Creating a Cyanotoxin Target List for the UCMR (PDF) (17 pp, 110K, About PDF) 
WHO Cyanobacterial toxins: Microcystin-LR in Drinking-water
WHO Toxic cyanobacteria in water: A guide to their public health consequences, monitoring and management
Current approaches to cyanotoxin risk assessment, risk management and regulations in different countries
WHO Guidelines for Safe Recreational Waters Volume 1 - Coastal and Fresh Waters
Health Canada Guidance for cyanobacterial Toxins – Microcystin-LR in Drinking Water
Health Canada Guidelines for Canadian Recreational Water Quality
Summary of the U.S. states with guidance values for cyanotoxins in drinking and recreational water 

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.

Links to State Information

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.

More Information

U.S. Environmental Protection Agency (EPA) Centers for Disease Control and Prevention (CDC)
  • This site provides information on cyanobacteria and HABs, CDC’s related activities and other HABs resources
National Oceanic and Atmospheric Administration (NOAA) U.S. Geological Service (USGS) Water Research Foundation Resources World Health Organization (WHO)

Association of State Drinking Water Administrators (ASDWA)

  • Nitrogen and Phosphorus "Nutrient" Pollution. This web page provides current information, resources, and links about nitrogen and phosphorus pollution (nutrient) issues, as well as current efforts being undertaken to document and address them.


Health Canada, Environmental and Workplace Health World Resources Institute, Eutrophication and Hypoxia, Nutrient Pollution in Coastal Water
  • Provide links and resources on HABs in coastal waters.

Intergovernmental Oceanographic Commission of UNESCO, Harmful Algal Bloom Programme

  • IOC Harmful Algal Bloom Website.

For comments, feedback or additional information, please contact Lesley D'Anglada (, Project Manager, at 202-566-1125.