Mercury is one of the most dangerous toxicants for all living organisms, having a high degree of biomagnification. The determination of mercury concentration in different species of fish is important for evaluation of the state of aquatic ecosystems. The aim of research is study of peculiarities of mercury content in fish of the Sheksna Reservoir, the Sukhona River, Kubenskoye, Borovskoye and Svyatoye lakes. Mercury concentration in fish muscles of the Vologda Region varies from 0.0397 mg/kg to 1.167 mg/kg of wet mass. The highest average of mercury content is established in the muscle tissue of river bass (0.477±0.202), and the lowest average is in the muscle tissue of eastern bream (0.133±0.082). Mercury level does not exceed maximum permissible concentration of heavy metal and weekly norm, harmless for a person weighing 70 kg in most of examined specimens. Сomparison of mercury content in muscles of fish from surveyed water bodies showed a significant difference between river bass and most non-piscivorous species, as well as between individuals of river bass from Svyatoye and Borovskoye lakes. We also revealed a reliable correlation dependence of mercury content in the muscle tissue on mass and length of body for samples of river bass, northern pike and silver bream. Values of mercury concentration in the muscle tissue of river bass from Lake Kubenskoye and the Sheksna Reservoir vary in process of time.