Microcystin (MC) accumulation was determined in the liver and muscle of two omnivorous fish species which are consumed and are economically important, and in a planktivorous-carnivorous fish from Lake Eğirdir, Turkey. Free extractable MCs in fish tissue samples were detected by enzyme-linked immunosorbent assay (ELISA) with confirmation by high performance liquid chromatography with photodiode array detection (HPLC-PDA). MC-LA and -YR, were detected in both liver and muscle, followed by MCs -LY, -LF, -RR and -LR respectively. The MC concentrations varied between 0.043 and 1.72 μg/g dry weight in liver and muscle tissues. MCs were also determined in samples of water, sediment and a bloom sample of Microcystis aeruginosa from the lake by HPLC-PDA. MC-LY and -YR were most commonly identified in water samples, with total MC concentrations ranging from 2.9 ± 0.05 to 13.5 ± 2.3 μg/L. Sediment analyses, showed that MC-YR was present in samples between 7.0 and 17.6 μg/g dw, especially in October, November and December when no MC-YR was recorded in water, followed by MC-LW. The findings indicate that water and sediment contained MCs, and more importantly that fish were contaminated with MCs that may pose an MC-associated human health risk.