Microcystins (MCs) are hepatotoxic heptapeptides released into water during or on senescence of cyanobacterial blooms. This review details the different effects of the MCs on fish and discusses their potential consequences in aquatic food webs. In early life stages, exposure to MCs causes, in a dose-dependent manner, perturbations to embryonic hatching, decrease in survival and growth rate, as well as histopathological effects (enlarged and opaque yolk sac, small head, curved body and tail, hepatobiliary abnormalities, ultrastructural alterations in hepatocytes, heart rate perturbations). In adults and juveniles, field and experimental studies demonstrated that after ingestion MCs accumulate mainly in liver but can also be found in muscle and viscera. Microcystin exposure has been shown to affect growth rate and osmoregulation, increase liver enzyme activities in the serum and heart rate, modify behavior, and exert histopathological effects in the liver, intestine, kidneys, heart, spleen, or gills, but the degree to which these effects were seen depends on the exposure route. The detoxication pathway of MCs in fish begins with a conjugation reaction to glutathione catalyzed by glutathione S-transferases, and this is comparable to the reaction demonstrated in other organisms, from plants to mammals. It appears that MC concentrations found in nature can potently affect several trophic levels in the aquatic ecosystems, in particular by inducing failure of sensitive stages (e.g., fish fry) to develop and accumulating in the food chains. The need of further quantitative studies on the sublethal effects, accumulation, and fate of MCs in aquatic food chains still remains.