This article concerns problems with the eutrophicated water treatment process. The main thread of the article is dedicated to some causes and risks which are associated especially with many organisms living in polluted reservoirs. The main threat in particular comes from the toxic substances produced by Cyanophyta that is directly connected with its living processes which complicates the whole water treatment process. The presence of Cyanophyta in water is a source of organic carbon and contributes to disinfection by-products. This work provides the examples of improving water treatment technology for water with excessive number of phytoplankton.