In summer 2007 water samples were collected in three lakes situated in the region of the Great Mazurian Lakes (northeastern Poland) displaying different types of catchment area: Lake Niegocin, Lake Piłwąg and Lake Rekąty. The main objective of this study was to analyze the difference in species composition of cyanobacteria and to determine the concentration of cyanotoxins. Potentially toxic species of cyanobacteria were found to be the dominant species in each sample. Microcystis aeruginosa was dominant in Lake Niegocin, Limnothrix redekei and Planktolyngbya limnetica in Lake Piłwąg, and Planktothrix agardhii in Lake Rekąty. Furthermore, the occurrence of an invasive cyanobacteria species, Cylindrospermopsis raciborskii, was detected in two lakes, Rekąty and Piłwąg. The toxin concentration in all of the samples did not exceed the guideline value of 5 μg·l^-1 recommended by the World Health Organization for recreational waters, which may indicate the dominance of non-toxic strains.