United States

Environmental Protection 

Agency

Office of Water

4304T

EPA-810F11001

 July, 2012 

Cyanobacteria and Cyanotoxins:

Information for Drinking Water Systems 

This fact sheet provides public water suppliers basic information on human health effects, 

analytical screening tools, and the effectiveness of various treatment processes to remove or 

inactivate the three most important cyanotoxins that can occur in the waters of almost every part 

of the US and are listed on the third Candidate Contaminant List (CCL): microcystin-LR, 

anatoxin-a, and cylindrospermopsin. Other cyanotoxins such as saxitoxins and anatoxin-a(S) also 

occur in US waters, but they are generally thought to be less common. Therefore, this fact sheet 

does not address these other well known toxins produced by cyanobacteria such as the paralytic 

shellfish toxins (Saxitoxin family), anatoxin-a(S), the lyngbyatoxins, or taste and odor 

contaminants caused by the cyanobacteria. 

 

Background

The Safe Drinking Water Act (SDWA) protects public health by regulating the nation's public 

drinking water supply and its sources: rivers, lakes, reservoirs, springs, and ground water wells. 

The SDWA requires the U.S. Environmental Protection Agency (EPA) to publish a list of 

unregulated contaminants that are known or expected to occur in public water systems in the US 

that may pose a risk in drinking water. This list is known as the Contaminant Candidate List 

(CCL). For more information on the CCL program go to 

http://water.epa.gov/scitech/drinkingwater/dws/ccl/

The cyanotoxins included in the most recent CCL are produced by several species of 

cyanobacteria (cyanobacteria are known as blue-green algae). The most widespread of the 

cyanotoxins are the peptide toxins in the class called microcystins. There are at least 80 known 

microcystins, including Microcystin-LR, which is generally considered one of the most toxic. 

More than a dozen countries (including Canada, Brazil, New Zealand, and Australia) have 

developed regulations or guidelines for microcystins in drinking water and recreational waters. 

Most of the drinking water guidelines are based on the World Health Organization provisional 

value for drinking waters of 1.0 μg/L microcystin-LR. No federal regulatory guidelines for 

cyanobacteria or their toxins in drinking water or recreational waters exist at this time in the 

United States.

Causes of cyanobacteria harmful algal blooms 

Cyanobacteria are photosynthetic bacteria that share some properties with algae and are found 

naturally in lakes, streams, ponds, and other surface waters. Similar to other types of algae, 

when conditions are favorable, cyanobacteria can rapidly multiply in surface water and cause 

"blooms." The conditions that enhance the growth of cyanobacteria are described below. Several 

types of cyanobacteria, like for example Anabaena flos-aquae, have gas-filled cavities that allow 

them to float to the surface or to different levels below the surface, depending on light conditions 

and nutrient levels. This causes the cyanobacteria to concentrate on the water surface, causing 
the typical pea-soup green color or blue-green "scum." Some cyanobacteria like Planktothrix 

agardhii, can be found in bottom sediments and float to the surface when mobilized by storm 

events and other sediment disturbances. Other cyanobacteria blooms may remain dispersed 

through the water column (Cylindrospermopsis sp.) leading to a generalized discoloration of the 

water. 

Factors that affect cyanobacterial bloom formation and persistence include light intensity and 

total sunlight duration, nutrient availability (especially phosphorus), water temperature, pH, an 

increase in precipitation events, water flow (whether water is calm or fast-flowing), and water 

column stability. Although bloom conditions in much of the US are more favorable during the 

late summer, the interrelationship of these factors causes large seasonal and year-to-year 

fluctuations in the cyanobacteria levels. Some toxin-producing strains can occur early in the 

summer season while others are only found during late summer. 

Cyanobacterial blooms can be harmful to the environment, animals, and human health. The 

bloom decay consumes oxygen, creating hypoxic conditions which result in plant and animal 

die-off. Under favorable conditions of light and nutrients, some species of cyanobacteria produce 

toxic secondary metabolites, known as cyanotoxins. Common toxin-producing cyanobacteria are 

listed in Table 1. The conditions that cause cyanobacteria to produce cyanotoxins are not well 

understood. Some species with the ability to produce toxins may not produce it under all 

conditions. These species are often members of the common bloom-forming genera. Both nontoxic and toxic varieties of most of the common toxin-producing cyanobacteria exist, and it is 

impossible to tell if a species is toxic or not toxic by looking at it. Also, even when toxinproducing cyanobacteria are present, they may not actually produce toxins. Furthermore, some 

species of cyanobacteria can produce multiple types and variants of cyanotoxins. Molecular tests 

are available to determine if the cyanobacteria, Microcystis for example, carry the toxin gene; 

quantitative cyanotoxin analysis is needed to determine if the cyanobacteria are actually 

producing the toxin. Water contaminated with cyanobacteria can occur without associated taste 

and odor problems. 

In most cases, the cyanobacteria toxins exist intracellularly in the cytoplasm and are retained 

within the cell. Anatoxin-a and the microcystin variants are found intracellularly approximately 

95% of the time during the growth stage of the bloom. For those species, when the cell dies or 

breaks, the cell membrane ruptures and the toxins are released into the water (extracellular 

toxins). However, in other species, cylindrospermopsin fo example, a significant amount of the 

toxin may be naturally released to the water by the live cyanobacterial cell; the reported ratio is 

about 50% intracellular and 50% extracellular. Extracellular toxins may absorb to clays and 

organic material in the water column and are generally more difficult to remove than the 

intracellular toxins.

Health effects caused by cyanotoxins 

The cyanotoxins include neurotoxins (affect the nervous system), hepatotoxins (affect the liver), 

and dermatoxins (affect the skin). The presence of high levels of cyanotoxins in recreational 

water and drinking water may cause a wide range of symptoms in humans (Table 1) including 

fever, headaches, muscle and joint pain, blisters, stomach cramps, diarrhea, vomiting, mouth 

ulcers, and allergic reactions. Such effects can occur within minutes to days after exposure. In

severe cases, seizures, liver failure, respiratory arrest, and (rarely) death may occur. There is 
Table 1. Cyanotoxins on the Contaminant Candidate List (CCL)

Cyanotoxin 

Number of 

known 

variants or 

analogues 

Primary 

organ 

affected

Health Effects1

Most common 

Cyanobacteria 

producing toxin2

Microcystin-LR 80~90 Liver Abdominal pain

Vomiting and diarrhea

Liver inflammation and 

hemorrhage

Acute pneumonia

Acute dermatitis

Kidney damage

Potential tumor growth 

promotion

Microcystis

Anabaena

Planktothrix

Anabaenopsis

Aphanizomenon

Cylindrospermopsin 3 Liver

Cylindrospermopsis

Aphanizomenon

Anabaena

Lyngbya

Rhaphidiopsis

Umezakia

Anatoxin-a group3

2-6 Nervous 

System

Tingling, burning, numbness, 

drowsiness, incoherent speech, 

salivation, respiratory 

paralysis leading to death

Anabaena

Planktothrix

Aphanizomenon

Cylindrospermopsis

Oscillatoria 1

Source: Harmful Algal Research and Response National Environmental Science Strategy (HARRNESS) 2 Not all species of the listed genera produce toxin; in addition, listed genera are not equally as important in producing 

cyanotoxins.

3

The anatoxin-a group does not include the organophosphate toxin anatoxin-a(S) as it is a separate group. In the US, the most 

common member is thought to be anatoxin-a, and thus this toxin is listed specifically.

evidence that long-term exposure to microcystins and cylindrospermopsin may promote the 

growth of tumors and may cause cancer. 

There have been many documented reports of dog, bird and livestock deaths throughout the 

world as the result of consumption of surface water with cyanobacterial blooms. Infrequently, 

human deaths have also been documented. Patients exposed intravenously to water containing 

microcystins in a kidney dialysis center in Brazil in 1996 resulted in 50 deaths. The actual risk to 

cyanotoxins at low levels in drinking water and the long-term effects to the exposure to these

toxins is uncertain. 

Screening Methods

Table 2 describes the methods available for cyanotoxin measurement in freshwater. There are 

commercially field test kits available for use as a screening tool to determine the presence or 

absence of specific cyanotoxins in a water supply. Screening kits (ELISA kits) are available for 

the microcystins, cylindrospermopsin and saxitoxin, but are not currently available for anatoxina. Although they provide rapid results, generally these kits have limitations in accuracy, 

sensitivity, and specificity. If the screening test is positive, the water system should send samples 

to a laboratory capable of measuring the concentrations of specific 
Table 2. Methods Available for Cyanotoxin Detection* 

 Freshwater Cyanotoxins 

Methods Anatoxins Cylindrospermopsins Microcystins

Biological Assays 

Mouse Yes Yes Yes

Protein Phosphatase Inhibition Assays 

(PPIA) No No Yes

Neurochemical Yes No No

Enzyme-Linked Immunosorbent Assays 

(ELISA) In progress Yes Yes

Chromatographic Methods 

Gas Chromatography 

Gas Chromatography with Flame Ionization 

Detection (GC/FID) Yes No No

Gas Chromatography with Mass 

Spectrometry (GC/MS) Yes No No

Liquid Chromatography

Liquid Chromatography / Ultraviolet-Visible 

Detection (LC/UV or HPLC) Yes Yes Yes

Liquid Chromatography/Fluorescence 

(LC/FL) Yes No No

Liquid Chromatography combined with mass spectrometry 

Liquid Chromatography Ion Trap Mass 

Spectrometry (LC/IT MS) Yes Yes Yes

Liquid Chromatography Time-of-Flight Mass 

Spectrometry (LC/TOF MS) Yes Yes Yes

Liquid Chromatography Single Quadrupole 

Mass Spectrometry (LC/MS) Yes Yes Yes

Liquid Chromatography Triple Quadrupole 

Mass Spectrometry (LC/MS/MS) Yes Yes Yes

*

Adapted from Analytical Methods for Cyanotoxin Detection and Impacts on Data Interpretation, presentation by Keith Loftin, 

Jennifer Graham, Barry Rosen (U.S. Geological Survey) and Ann St. Amand (Phycotech) at the 2010 National Water Quality 

Monitoring Conference, Workshop. Guidelines for Design, Sampling, Analysis and Interpretation for Cyanobacterial Toxin 

Studies at Denver, CO on April 26, 2010.

cyanotoxins using more accurate techniques such as Liquid Chromatography combined with 

Mass Spectrometry (LC/MS). 

Cyanotoxin Treatment and Bloom Management 

Once cyanobacteria and/or their cyanotoxins are detected in the surface water supplying the 

water system, the treatment system operators can act to remove or inactivate them in a number of 

ways. Some treatment options are effective for some cyanotoxins, but not for others. Therefore, 

drinking water operators must know the growth patterns and species of cyanobacteria that 

dominates the bloom, the properties of the cyanotoxins (i.e., intracellular or extracellular), and 

the most effective treatment process. Applying the wrong treatment process at a specific state in 

treatment could damage cells and result in the release rather than removal of cyanotoxins. 
Table 2 summarizes the effectiveness of different types of water treatment to remove intact 

cyanobacteria cells and treatment processes that are effective in removing extracellular dissolved 

toxins of several of the most important cyanobacteria. Drinking water operators are encouraged 

to monitor the treated water to guarantee the removal of cyanotoxins. 

To avoid the release of cyanotoxins into the water, drinking water operators can undertake 

different management strategies to deal with cyanobacteria blooms. For example, those drinking 

water utilities that have access to more than one source of water supply, an alternative is to 

change sources. Another management alternative is to adjust intake depth to avoid drawing 

contaminated water and cells into the treatment plant. 

Pretreatment oxidation at the intake, although often used to reduce taste and odor compounds 

and to reduce zebra mussels and to reduce other contaminants, poses several concerns with 

respect to breaking cells and releasing toxins. Copper sulfate and ozone at the intake removes the 

algal bloom, but is not recommended because of the risk of lysing algal cells. Chlorination, in 

addition to breaking the cells, has the potential to produce disinfection by-products during water 

treatment. If pretreatment oxidation is needed, potassium permanganate (KMnO4) has been 

demonstrated to be effective in removing Microcystis cells with no release of toxin. It is 

recommended that powdered activated carbon (PAC) be used in addittion to remove any toxins 

that may have been released. 

The standard drinking water treatment processes (coagulation, flocculation, sedimentation and 

filtration), have shown to be effective in removing intracellular cyanotoxins. Coagulation, 

flocculation and dissolved air flotation (DAF), are more effective than sedimentation.

Microfiltration and ultrafiltration are highly effective at removing intact cyanobacterial cells. 

When a bloom occurs and cells are carried through to the filters, backwash should be more 

frequent to reduce the risk of toxins release in the water. 

For removal of extracellular toxins, drinking water operators may use activated carbon, 

membrane filtration and chemical inactivation (Ultraviolet (UV), disinfectants and oxidants). 

Both powdered activated carbon (PAC) and granular activated carbon (GAC) have been effective 

in absorbing microcystin and cylindrospermopsin, although microcystin variants may have 

different adsorption efficiencies. The performance of activated carbon depends on the 

concentration of the toxin and the dose and origin of the activated carbon. Jar tests are

recommended to test the effectiveness of various PAC types, with the implementation of the 

carbon with the greatest capacity for removal of the target contaminants. GAC filters are 

effective in removing microcystins if they are properly replaced or regenerated when total 

organic carbon breakthrough is high. Usually, higher concentrations of activated carbon are

necessary to effectively remove toxins; repeated treatment may be needed to totally remove the 

toxins completely. Nanofiltration and reverse osmosis are effective in removing 

cylindrospermopsin and microcystin. However, site specific tests are recommended as removal 

efficiency depends on the membrane pore size distribution and water quality. 

Ultraviolet (UV) treatment is effective in destroying microcystin, anatoxin-a, and 

cylindrospermopsin cells but higher doses than are practicable are required, making it a not 

viable treatment. UV has been used along with a catalyst (titanium dioxide) to oxidatively 

decompose the toxins. However, the effectiveness of this process is largely dependent on the 
Table 2. Cyanotoxin Treatment Processes and Relative Effectiveness 

Treatment Process Relative Effectiveness

Intracellular Cyanotoxins Removal (Intact Cells) 

Pretreatment oxidation Avoid pre-oxidation because often lyses cyanobacteria cells releasing the cyanotoxin to the water column. 

Coagulation/Sedimentation/ 

Filtration

Effective for the removal of intracellular toxins when cells accumulated in sludge are isolated from the plant 

and the sludge is not returned to the supply after sludge separation. 

Membranes

Study data is scarce; it is assumed that membranes would be effective for removal of intracellular 

cyanotoxins. Microfiltration and ultrafiltration are effective when cells are not allowed to accumulate on 

membranes for long periods of time. 

Flotation Flotation processes, such as Dissolved Air Flotation (DAF), are effective for removal of intracellular 

cyanotoxins since many of the toxin-forming cyanobacteria are buoyant. 

Oxidation processes Avoid because often lyses cyanobacteria cells releasing the cyanotoxin to the water column. 

Extracellular Cyanotoxins Removal 

Membranes

Depends on the material, membrane pore size distribution, and water quality. Nanofiltration and ultrafiltration 

are likely effective in removing extracellular microcystin. Reverse osmosis filtration would likely only be 

applicable for removal of some extracellular cyanotoxins like cylindrospermopsin. Cell lysis is highly likely. 

Further research is needed to characterize performance. 

Potassium Permanganate Effective for oxidizing microcystins and anatoxins. Further research is needed for cylindrospermopsin. 

Ozone Very effective for oxidizing extracellular microcystin, anatoxin-a and cylindrospermopsin. 

Chloramines Not effective

Chlorine dioxide Not effective with doses used in drinking water treatment. 

Chlorination Effective for oxidizing extracellular cyanotoxins as long as the pH is below 8, ineffective for anatoxin-a.

UV Radiation Effective of degrading microcystin and cylindrospermopsin but at impractically high doses.

Activated Carbon

PAC: Most types are generally effective for removal of microcystin, anatoxin-a and cylindrospermopsin, 

especially wood-based activated carbon.

GAC: Effective for microcystin but less effective for anatoxin-a and cylindrospermopsins. 
organic content of the water. Oxidants like chlorine, ozone and KMnO4 are effective 

mechanisms for inactivation of microcystin but chlorine effectiveness is pH-dependent. Different 

cyanotoxins react differently to chlorine, for example, it has proved to be ineffective for the 

inactivation of anatoxin-a. However, when pH is below 8, chlorine is effective for inactivation 

of microcystin and cylindrospermopsin. Ozone is a good oxidant of microcystins, anatoxin-a and 

cylindrospermopsin, but its efficacy is also ph-dependent and may be affected by the presence of 

organic matter. Although ozone is ph-independent for the oxidation of microcystin, is pHdependent for the oxidation of anatoxin-a (pH 7 to 10) and for cylindrospermopsin (4 and 10). 

KMnO4 is effective in oxidizing microcystin and anatoxin-a (from pH 6 to 8), but is not very 

reactive with cylindrospermopsin. Chloramines and chlorine dioxide are not effective treatments 

for microcystin, anatoxin-a and cylindrospermopsin. 

Formation of disinfection by-products is another potential problem with the use of ozone, copper 

sulfate, and chlorine when there are high bromide concentrations in the water. However, results 

from studies on the impact of chlorination of cell-bound toxins and resulting disinfection byproducts formation are contradictory. The majority of the findings suggest that pre-chlorination 

should ideally be avoided during blooms, unless adequate CT values can be guaranteed to ensure 

efficient oxidation of broken cyanobacteria. 

Developing a Contingency Plan

Water supply managers should develop a contingency plan when cyanobacterial blooms may 

occur. Most algal blooms are not toxic, and the plan should address how to determine the risk 

associated with each event. Elements of such a plan should include determining when and where 

to sample; sampling frequency; sample volume; whether to sample for cyanobacterial cells or 

specific cyanotoxins or both; which analytical screening test to use; and conditions when it is 

necessary to send sample(s) to an identified laboratory for confirmation. Drinking water system 

operators should also develop alternative plans for treatment before results are known; including 

what treatment option(s) to use if test results are positive; and identifying a process for public 

notification. Chapter 6 (Situation Assessment, Planning and Management) from the WHO’s 

Toxic Cyanobacteria in Water: A guide to their public health consequences, monitoring and 

management could be used as a resource to develop such plans. 

Where can I get more information? 

For more information, please visit the Cyanobacteria Harmful Algal Blooms (CyanoHABs) web 

page at http://www.epa.gov/nandppolicy/links.html#hab .

Acknowledgements

The author gratefully acknowledges the valuable contribution from Dr. Judy Westrick, Lake 

Superior State University, in developing this work. 
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