Mercury, which tends to bioaccumulate and biomagnify in aquatic food webs, poses a potential health risk to wildlife and to consumers of predatory fish in particular. Its concentration in biota can be high even at low environmental concentrations. Therefore, the aim of this study was to determine mercury in both abiotic (water and sediment) and biotic elements (common reed (Phragmites australis) and fish: pike (Esox lucius), bream (Abramis brama) and roach (Rutilus rutilus)) in the context of assessing the pollution of two lakes in Poland and the safety of fish consumers. The possibility of Hg biomagnification in fish was also considered. Mercury was determined by means of cold vapor atomic absorption spectrometry (CVAAS). The concentrations of Hg in water and bottom sediments of Lake Ińsko were lower than in Lake Wisola. In the bottom sediments of both lakes, a positive correlation was found between the Hg content and organic matter. The concentration of mercury in the organs of common reed did not exceed 0.017 mg/kg dry weight (dw), and its distribution can be presented as follows: root > leaves > stems > rhizomes. In fish organs from both lakes, the average mercury content did not exceed 0.086 mg/kg of wet weight (ww) and in most cases it was the highest in pike. Higher values were only observed in the muscles and skin of roach. This indicates a lack of biomagnification in the relationships between planktivorous-predatory and benthivores-predatory fish. Based on the maximum levels of mercury in fish and the calculated parameters, i.e., estimated daily intake (EDI), target hazard quotient (THQ) and tolerable weekly intake (TWI), the muscles of the examined fish were found to be safe for consumption. The average dietary exposure to total mercury (THg) and methylmercury (MeHg) was below 0.3% of the TWI.