Cyanobacteria are common in eutrophic natural waters. Being favoured by warm, stable and nutrient-enriched waters they may constitute an important part of the phytoplankton community in Wastewater Treatment Plants (WWTP). The phytoplankton communities of two ponds (facultative and maturation) of the WWTP of Esmoriz (North Portugal) were studied, with particular importance given to cyanobacteria. Mouse bioassays were performed with cyanobacteria samples during some of the blooms and ELISA assays specific for hepatotoxic microcystins were carried out. During the study period (January-July 1999) cyanobacteria were frequently dominant in the ponds ranging from 15.2 to 99.8% of the total phytoplankton density. The main species were Planktothrix mougeotii, Microcystis aeruginosa and Pseudanabaena mucicola. Mouse bioassays were performed during Oscillatoria bloom period but the results were negative, in spite of the high cyanobacteria biomass. ELISA assays were performed for both ponds but only in the maturation pond positive values were found. Microcystin concentrations (as MCYST-LR equivalents) varied from 2.3 to 56.0μg/l on the margin of the pond and between 1.7 and 4.6μg/l in the outflow of this pond. These values indicate that WWTP may be a source of contamination of water bodies with cyanobacteria toxins.