Cyanotoxins are produced by cyanobacteria, also known as blue-green algae. Cyanobacteria are found in all aquatic environments. In freshwater bodies an increase in nitrate and phosphate often results in vigorous cyanobacterial growth, producing a bright-green surface layer and surface scum, a condition referred to as a "harmful algal bloom" (HAB). The HABs result in the presence of significant numbers of dead and lysed cyanobacterial cells that spill their contents, including cyanotoxins such as anatoxin-a, anatoxin-as, cylindrospermopsin, microcystins and nodularin, into the water.

Anatoxin-a is a potent neurotoxin that acts as acetyl choline agonist, causing irreversible muscle contraction, and is produced by Anabena flos-aquae, A. planktonica, as well as Oscillatoria, Aphanizomenon and Cylindrospermum species. The LD₅₀ of anatoxin-a is 200 µg/kg body weight. Anatoxin-as, which is structurally unrelated to anatoxin-a, is also a neurotoxin, but is produced by Anabaena lemmermannii, and is significantly more toxic, exhibiting an LD₅₀ of 20 µg/kg body weight.

Cylindrospermopsin is produced by Cylindrospermopsis raciborskii and has an LD₅₀ of 200 µg/L.

The microcystins are cyclic heptapeptides composed of five non-protein amino acids, and two protein amino acids and are found in Microcystis, Anabaena, Oscillatoria, Nodularia, Nostoc, Cylindrospermopsis, and Umezakia species. Over 80 different microcystins have been identified. The microcystins are potent hepatotoxins. Microcystin-LR has an oral LD₅₀ of 50 µg/kg body weight in rats. It inhibits the enzymes phosphatase 1 and 2A and activates phosphorylase b. This results in the death of hepatocytes, the most abundant liver cell, leading to significant liver swelling and extensive intrahepatic hemorrhage. There is no known cure for microcystin-LR poisoning. Microcystins are highly water soluble and very resistant to breakdown, retaining toxicity even after boiling the water. The half-life of a typical microcystin under ambient conditions is 10 weeks.

The nodularins are related to the microcystins in that they are also cyclic peptides and potent hepatotoxins. Nodularin-R is a cyclic peptapeptide produced by Nodularia spumigena. The LD₅₀ of nodularin-R was reported as 50 µg/kg body weight in mice. A few structural variants have been identified. Nodularin-Har has a reported LD₅₀ of 70 µg/kg body weight in mice.

The World Health Organisation (WHO) has published a comprehensive guide on the danger and management of cyanotoxins in drinking water. The WHO also recommended a provisional guideline value of 1 µg/L for microcystin-LR in drinking-water. A guideline value for cylindrospermopsin is currently under review at the WHO.

Although not currently regulated in the US, the Environmental Protection Agency has included anatoxin-a, microcystin-LR, and cylindrospermopsin in its Contaminant Candidate List 3, a list of contaminants released in September 2009, that may require regulation under the Safe Drinking Water Act.

The Water Quality Guideline, published by the Department of Water Affairs in South Africa, recommends microcystin levels <0.8µg/L in domestic drinking water.