Toxin-producing cyanobacteria in lakes and reservoirs form a threat to humans as well as various forms of aquatic life. This study is an investigation into the occurrence and distribution of Microcystins (MCYST) in 13 Greek Lakes. The distribution of MCYST in water and surface scum and toxin bioaccumulations in the omnivorous fish species Carassius gibelio were surveyed in all lakes. Considerable amounts of MCYST were found in water and scum of all lakes, irrespective of the trophic state, the type of the lake, and the reported dominant cyanobacterial species. Toxin accumulation in six tissues (liver, brain, intestine, kidney, ovary, and muscle) of C. gibelio was also analyzed. Even though the target organ for MCYST is the liver, in our study, MCYST were found also in the rest of C. gibelio tissues in the following order: liver > intestine > kidney > brain > ovaries > muscle. Risk assessments were carried out, taking into account the WHO guidelines and the tolerable daily intake (TDI) for MCYST. Our findings suggest that the amounts of MCYST found in water of Lakes Kastoria, Koronia, Pamvotis, Doirani, Mikri Prespa, Petron, and Zazari, pose adverse health risks. Also, it is likely to be unsafe to consume C. gibelio in Lakes Koronia, Kastoria, Pamvotis, and Mikri Prespa due to the high concentrations of accumulated MCYST.