Causes and Prevention

Cyanobacteria occur naturally in freshwater and have been present in aquatic ecosystems for a very long time, with their first occurrence dating back at least 2.7 billion years ago. Cyanobacteria are generally present, but not necessarily dominant—i.e., present in large quantities as blooms—in freshwater bodies in the United States. There are many physical and chemical factors that contribute to the formation and persistence of cyanobacterial blooms in freshwater systems in the U.S.

What are some causes of cyanobacterial blooms?

Some physical factors that contribute to the creation of harmful algal blooms (HABs) 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 that occur largely on seasonal time scales. 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).

How do human activities affect cyanobacterial blooms?

There is widespread agreement within the scientific community that the incidence of HABs is increasing both in the U.S. and worldwide. This recent increase in the occurrence of HABs has been attributed to increasing anthropogenic activities and their interaction with the factors that are known to contribute to the growth of cyanobacterial blooms. 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, anthropogenic climate change has recently been identified as a contributing factor to cyanobacterial blooms.

How will global climate change affect cyanobacterial blooms?

Climate change will alter many environmental conditions that have the ability to affect the natural properties of fresh and marine waters both in the U.S. and worldwide. Recent research suggests that, in addition to nutrient contamination from anthropogenic sources, the impacts of climate change may promote the growth and dominance of HABs through a variety of mechanisms including, but not limited to:

  • Warmer water temperatures
  • Changes in salinity
  • Increases in atmospheric carbon dioxide concentrations
  • Changes in rainfall patterns
  • Intensifying of coastal upwelling
  • Sea level rise
Flowchart of controlling harmful cyanobacterial blooms
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.

The following conceptual figure illustrates the environmental processes that control cyanobacterial blooms, including man-made management actions and impacts of climate change.

For more information on the effect of climate change on the occurrence of HABs, please visit the EPA's fact sheet on Climate Change and Harmful Algal Blooms.

What measures can be taken to prevent cyanobacterial blooms?

Preventative measures are the preferred approach to managing the occurrence of cyanobacterial blooms. 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.

More Information

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.

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