Control and Treatment

The control and management of cyanobacteria in surface water and treatment of cyanotoxins in drinking water is critical to protect human health. There are several methods that watershed managers and treatment system operators can use to help avoid and remediate cyanobacterial harmful algal blooms (HABs).

What are some preemptive management measures for cyanobacterial blooms in surface waters?

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.

Additional preemptive management measures are applicable on the watershed level. Various measures target nutrient input from 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). Several drawbacks to this watershed approach are that it does not consider internal nutrient loads that cycle from sediment to the water column, it is difficult to implement over large areas, and it does not address several of the small-scale environmental factors that contribute to cyanobacterial blooms.

What are some mitigation measures for the presence of HABs in surface waters?

Toxic Algae Infographic
An infographic illustrating the effects of anthropogenic nutrient runoff on HABs and potential solutions to these issues. Source:

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.

Biological mitigation measures include different approaches to change the aquatic food web in an attempt to increase grazing pressure on cyanobacteria through the introduction of functionally competitive species (e.g., diatoms). Competition and grazing can affect the net growth rates of algae in water, but the effectiveness of reducing harmful algae depends on its population density and the ambient nutrient concentration. 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, further research is necessary in order to fully understand the impact of phytoplankton grazing. The table below provides a summary of the common mitigation practices for cyanobacteria in surface waters.

To further the goals of protecting sources of drinking water, federal, state, and local partners, has come together to form the Source Water Collaborative, a group of 26 national organizations originally formed in 2006 with the goal to combine the strengths and tools of a diverse set of member organizations to protect drinking water sources for generations to come. The Source Water Collaborative supports activities to reduce HABs risk factors through member-to-member information sharing, development of recommendations and educational materials, and dissemination of information through member networks, the Source Water Collaborative website, and social media. Member organizations engage in a wide range of actions to reduce HABs risk factors through land management and nutrient reduction.

A Summary of Waterbody Management Methods for Cyanobacterial Blooms

Waterbody Management Method Description Benefits/Effectiveness Limitations
 Physical Controls
 Aeration Aerators operate by pumping air through a diffuser near the bottom of the waterbody, resulting in the formation of plumes that rise to the surface and create vertical circulation cells as they propagate outwards from the aerator. This mixing of the water column disrupts the behavior of cyanobacteria to migrate vertically in addition to limiting the accessibility of nutrients. Successfully implemented in small ponds and waterbodies. Proven effectiveness in several field studies. May also provide more favorable growth conditions for competing organisms. Generally more efficient in deeper water columns. Also highly dependent upon the degree of stratification and the air flow rate.
 Hydrologic manipulations Low flow conditions in waterbodies can lead to stratification of the water column, which aids cyanobacterial growth. Particularly in regulated systems, the inflow/outflow of water in the system can be manipulated to disrupt stratification and control cyanobacterial growth. Easy to implement in controlled systems (i.e., reservoirs, dams, treatment facilities). Requires sufficient water volume and the ability to control flow. Oftentimes can be expensive. Unintended consequences for other aquatic organisms are likely.
 Mechanical mixing (circulation) Mechanical mixers are usually surface-mounted and pump water from the surface layer downwards or draw water up from the bottom to the surface layer. This mixing of the water column disrupts the behavior of cyanobacteria to migrate vertically in addition to limiting the accessibility of nutrients. Successfully implemented in 350+ waterbodies in the U.S. Also used in other countries. Individual devices have limited range; areas further away may remain stratified and provide a suitable environment for growth.
 Reservoir drawdown/dessication In reservoirs and other controlled waterbodies, can draw down the water level to the point where cyanobacteria accumulations are exposed above the waterline. Subsequent dessication and/or scraping to remove the layer of cyanobacteria attached to sediment or rock is required, in addition to the reinjection of water into the system. Easy to implement in controlled systems (i.e., reservoirs, dams, treatment facilities). Can have a significant impact on other aquatic organisms in the system. Often times is expensive and requires a significant input of resources.
 Surface skimming Cyanobacterial blooms often form surface scums, especially in the later stages of a bloom. Oil-spill skimmers have been used to remove cyanobacteria from these surface scums. Often times this technique is coupled with the implementation of some coagulant or flocculant. Useful method for blooms that are in later stages and have formed surface scums. Successful results seen in field studies in Australia. This technique cannot be effectively employed until the later stages of a bloom, at which point many of the harmful aspects of a bloom have materialized. Requires proper equipment prior to implementation.
 Ultrasound An ultrasound device is used to control HABs by emitting ultrasonic waves of a particular frequency such that the cellular structure of cyanobacteria is destroyed by rupturing internal gas vesicles used for buoyancy control. Successfully implemented in ponds and other small waterbodies. A single device can cover up to 8 acres. Non-chemical; inexpensive. Also disrupts cellular functioning of green algae. Effectiveness are dependent upon waterbody geometry and cyanobacteria species. Further research of method is required.
 Chemical Controls
 Algaecides Algaecides are chemical compounds applied to a waterbody to kill cyanobacteria. Several examples are:
  • Copper-based algaecides (copper sulphate, copper II alkanolamine, copper citrate, etc.)
  • Potassium permanganate
  • Chlorine
  • Lime
Wide range of compounds with a history of implementation. Relatively rapid and well-established method. Properties and effects of compounds are typically well-understood. Risk of cell lyses and the release of toxins. Thus, is often used at the early stages of a bloom. Certain algaecides are also toxic to other organisms such as zooplankton, other invertebrates, and fish.
 Barley straw Barley straw bales are deployed around the perimeter of the waterbody. Barley straw, when exposed to sunlight and in the presence of oxygen, produces a chemical that inhibits algae growth. Field studies suggest significant algistatic effects. Several causes for the observed effects have been suggested; however, the exact mechanism of this process is not well understood. Studies have shown that decomposed barley straw inhibits the growth of cyanobacteria Microcystis sp. Successfully implemented in many reservoirs and dams in the United Kingdom with positive results. Does not kill existing algae, but inhibits the growth of new algae. May take anywhere from 2 to 8 weeks for the barley straw to begin producing active chemical. Potential to cause fish kills through the deoxygenation of the waterbody due to decay.
 Coagulation Coagulants are used to facilitate the sedimentation of cyanobacteria cells to the anoxic bottom layer of the water column. Unable to access light, oxygen, and other critical resources, the cells do not continue to multiply and eventually die. Several studies have shown that cells can be coagulated without damage; however, further research is required. Successfully implemented in several treatment facilities. Subject to depth limitations. Coagulated cells become stressed over time and lyse, releasing toxins to the waterbody.
 Flocculation Flocculants are used to facilitate the sedimentation of nutrients to the anoxic bottom layer of the water column, thereby limiting nutrient levels in the waterbody and inhibiting cyanobacterial growth. Successfully implemented in larger lakes and ponds (e.g., Florida DEP, Lake Hilaman). Subject to depth limitations.
Hypolimnetic oxygenation Techniques used to achieve hypolimnetic oxygenation include: airlift pumps, side stream oxygenation and direct oxygen injection. The primary goal of this method is to increase the oxygen concentration in the hypolimnion in order to prevent or reduce the release of nutrients from the sediment while maintaining water column stratification. This serves to limit upper level nutrient levels thereby inhibiting cyanobacterial growth. Maintains water column structure (thermocline, pycnocline, etc.). Techniques are relatively expensive. Requires a significant understanding of system in order to determine effectiveness.
 Biological Controls (Biomanipulation)
Floating artificial wetlands Artificial wetlands are constructed using floating mats and placed in a waterbody. As the plants grow, they function as a sink for excess nutrients such as phosphorous and nitrogen. Periodic harvesting of mature plants is conducted to prevent the stored nutrients from re-entering the aquatic ecosystem, which helps to mitigate the risk of cyanobacterial blooms by keeping nutrient levels in balance.   Implemented in small waterbodies with limited success.  Often dependent upon the amount of input (i.e., the number of plants and mats). Also subject to depth limitations. 
Increasing grazing pressure Various measures can be introduced to encourage the growth of zooplankton, benthic fauna, and other aquatic organisms that feed on cyanobacteria, thereby limiting the proliferation of cyanobacteria populations. Techniques include:
  • The removal of fish that feed on zooplankton and other benthic fauna or the introduction of predators to these fish, and
  • The development of niches to encourage the growth of beneficial organisms.
Biomanipulation has fewer direct detrimental effects on other aquatic organisms when compared to chemical and physical methods.   Unintended consequences may arise related to the deliberate modification of the biodiversity of the system. Requires constant monitoring. Increasing resource competition has only proven effective in shallow water bodies with moderate nutrient levels
Increasing resource competition The introduction of other primary producers such as macrophytes can limit the available phosphorus and therefore limit cyanobacterial growth. An example of this technique is the introduction of floating wetlands (see above).

What are some mitigation measures for the presence of HABs in drinking water supplies?

Cyanobacteria and cyanotoxins in drinking water supplies may also be mitigated during the treatment process. 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. See the table below for a summary of the various water treatment techniques used for cyanotoxin removal and their respective effectiveness.

A Summary of Cyanotoxin Treatment Processes and Their 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. If oxidation is required to meet other treatment objectives, consider using lower doses of an oxidant less likely to lyse cells (potassium permanganate). If oxidation at higher doses must be used, sufficiently high doses should be used to not only lyse cells but also destroy total toxins present (see extracellular cyanotoxin removal).
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 separation. 
 Membranes Study data is scarce; it is assumed that membranes would be effective for removal of intracellular cyanotoxins. 
 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 Avoid because often lyses cyanobacteria cells releasing the cyanotoxin to the supply. 
Extracellular Cyanotoxins Removal
 Membranes Depends on the material, membrane pore size, and water quality. Nanofiltration and ultrafiltration are likely effective in removing extracellular microcystin. Reverse osmosis filtration would likely only be applicable for the removal of some extracellular cyanotoxins like cylindrospermopsin. Cell lysis is highly likely. Further research is required to characterize performance. 
 Potassium Permanganate Effective for oxidizing microcystins and anatoxins. 
 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 for 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.  

Source: U.S. EPA, Office of Water: Cyanobacteria and Cyanotoxins: Information for Drinking Water Systems, September, 2014.

During the proliferation of a bloom, a substantial proportion of toxins are released to the water column. Furthermore, the application of algaecides in drinking water reservoirs may exacerbate this issue since the use of these substances leads to the further release of toxins through the lysing of cyanobacteria. 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.

What are some takeaways regarding the control/treatment of cyanobacteria?

Generally, mitigation and treatment techniques that are applied once a bloom has formed can be important management tools; however, preventing the bloom from forming when possible yields better results and is preferable to mitigation. A wide range of technologies are available for the treatment of drinking water sources contaminated with cyanotoxins, but it is clear that all of these technologies have specific trade-offs that must be carefully considered before implementation. Choosing the most efficient, safest, and cost-effective approach should be done on case-by-case basis. Water supply managers should develop a contingency plan including monitoring efforts such as 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. The plan should also include Management and Communication plans describing what treatment option(s) to use to reduce the potential of cyanotoxins in the finish water or reaching the distribution system; and identifying the required communication steps to coordinate with the agencies involved the appropriate actions that must be taken, and the steps to inform consumers and the public. 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 and the Incident Management Plans chapter from the International guidance manual for the management of toxic cyanobacteria (Water Quality Research Australia) could be used as resources to develop such plans.

More Information

A Water Utility Manager’s Guide to Cyanotoxins
The Lake and Reservoir Restoration Guidance Manual
Monitoring Lake and Reservoir Restoration, Technical Supplement
EPA Webinar Prevention, Control and Mitigation of CyanoHABs Presentations
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 MB)
Cyanobacteria and Cyanotoxins: Information for Drinking Water Systems Fact sheet 
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.

Top of Page