Eutrophication of surface water has increased significantly during the past decade, resulting in increased occurrences of toxic blooms. Cyanotoxins have become a global health threat to humans, wild animals, or domestic livestock. Hepatotoxic microcystins (MC) are the predominant cyanotoxins, which accumulate in aquatic organisms and are transferred to higher trophic levels. This is an issue of major concern in aquatic toxicology, as it involves the risk for human exposure through the consumption of contaminated fish and other aquatic organisms. The persistence and detoxification of MC in aquatic organisms are important issues for public health and fishery economics. Bioaccumulation of MC depends on the toxicity of the strains, mode of feeding, and detoxication mechanisms. Although mussels, as sessile filter feeders, seem to be organisms that ingest more MC, other molluscs like gastropods, as well as zooplankton and fish, may also retain average similar levels of toxins. Edible animals such as some species of molluscs, crustaceans, and fish present different risk because toxins accumulate in muscle at low levels. Carnivorous fish seem to accumulate high MC concentrations compared to phytophagous or omnivorous fish. This review summarizes the existing data on the distribution and dynamics of MC in contaminated aquatic organisms.