Cyanobacterial blooms and cyanotoxin production were studied for 2 years in four hydrologically modified lakes with nutrient-rich waters. We hypothesized that frequency of flushing may considerably influence cyanobacterial blooms. Abundance, biomass and diversity of cyanobacteria as well as cyanotoxins' variability and concentrations (by HPLC-PDA; -FLD) were determined. In two larger lakes, into which nutrient-rich water was supplied once a year, lower cyanobacterial species diversity, higher biomass of Microcystis spp., Aphanizomenon spp., Dolichospermum spp. and higher microcystin (MC) concentrations were found. In the other lakes, with several irregular water-level manipulations per year (alternating outputs and inputs), higher diversity, lower biomass of cyanobacteria and MC concentrations were observed. MC-LF, -LR and -RR produced by Microcystis spp. predominated in the more stable lakes, whereas in the lakes with frequent water manipulations different species of Oscillatoriales developed and MC-LA, -LY, -LW and -WR were also important. RDA analysis revealed that the frequency of water manipulations was the most significant variable for composition of cyanobacterial communities. The study highlights that a higher frequency of water-level manipulations, which increased flushing rate, was beneficial to nutrient-rich water reservoirs.