Quite a wide range of substances influencing the environment including water supplies are produced by cyanobacteria. The harmful products are called cyanotoxins and they can have impact on the both food and drinking water. The products of cyanobacteria mentioned in this article are, for example, oligosaccharides, organic acids, enzymes, antibiotics, various odors and toxins (cyanotoxins). Owing to long-term stability of the toxins, the high incidence of cyanobacteria in the environment and high toxicity of the toxins, the cyanobacteria represent an emerging problem. The present article critically summarizes the basic facts about the toxic products of cyanobacteria. It contains examples of toxins, case reports and discussion of cyanotoxins’ persistence in the environment.