Fish are a group of organisms that are highly sensitive to mercury (Hg) contamination of the aquatic environment. At the same time, because this element can be accumulated in tissues, it can pose a serious threat to human health. The main objective of the study was to determine the content of Hg in the muscles (HgM) and gills (HgG) of various species of fish from shallow lakes with varied physicochemical conditions. Sampling was done in 5 lakes from April to November 2012 and 2013. The concentration of Hg in fish tissues was affected by 4 variables, including ammonium nitrogen, chlorophyll-a, oxygen saturation, and temperature, and the first 2 axes explained 78.9% of total variance in Hg concentration. The concentration of Hg in muscles was widely varied depending on the fish species, and its highest concentration was observed in predatory fish such as asp and perch, while the lowest concentration of this element was found in Prussian carp, bream, and rudd. Although content of Hg increased with fish body length, in non-predatory fish this correlation was less clear. The gills of the fish contained lower concentrations of Hg than the muscles. Hg content in muscles was within acceptable weekly limits, but predatory fish consumed in large quantities by the local population may pose a potential risk for human health.