The objectives of this study were: (1) to examine the distribution and bioaccumulation of microcystins in the main components of the food web (phytoplankton, zooplankton, crayfish, shrimp, mussel, snail, fish, frog) of Lake Pamvotis (NW Greece), (2) to investigate the possibility of microcystin biomagnification and (3) to evaluate the potential threat of the contaminated aquatic organisms to human health. Significant microcystin concentrations were detected in all the aquatic organisms during two different periods, with the higher concentrations observed in phytoplankton and the lower in fish species and frogs. This is the first study reporting microcystin accumulation in the body of the freshwater shrimp Atyaephyra desmsaresti, in the brain of the fish species common carp (Cyprinus carpio) and in the skin of the frog Rana epirotica. Although there was no evidence for microcystin biomagnification, the fact that microcystins were found in lake water and in the tissues of aquatic organisms, suggests that serious risks to animal and public health are possible to occur. In addition, it is likely to be unsafe to consume aquatic species harvested in Lake Pamvotis due to the high-concentrations of accumulated microcystins.