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Planktonic, epiphytic and benthic cyanobacteria were investigated in June and September 2016 in the floodplain Lake Sakadaš (Kopački Rit Nature Park, Croatia). The hydrological regime strongly influenced the physico-chemical environment of the lake, as well as the diversity and abundance of cyanobacteria. Higher transparency (1.21 m) and nutrient concentrations (nitrates 6.77 mgN/L ; total phosphorus 2.823 mg/L and total nitrogen 9.31 mg/L) were observed in June during the flooding, while higher algal abundance and surface water chlorophyll concentrations (116.33 µg/L) were found in the conditions of low water level in September. Species of the genera Heteroleibleinia, Tolypothrix and Phormidium were the most abundant on metaphyton mats and sediment in June, accompanied by an invasive and potentially toxic Cylindrospermopsis raciborskii in epiphytic communities on Ceratophyllum demersum and sediment in September. Among planktonic cyanobacteria, Pseudanabaena, Planktothrix and Phormidium prevailed during the flooding, while in September, C. raciborskii bloom was observed. Due to their tolerance to a wide range of temperature, light and nutritional conditions, ability of cyanobacteria to colonize available niches in freshwater biotopes can be one of the strategies to cope with or adapt to changing climatic conditions.