Heavy metals are introduced into water due to anthropogenic activities and can significantly affect an entire ecosystem. Due to their close integration with the water environment, fish are a sensitive indicator of contamination. In addition, fish is an important element in human diets, therefore, monitoring the concentrations of metallic contaminants in their meat is particularly important for food safety. This study aimed to assess the pollution of water ecosystems with selected toxic heavy metals in lakes Dratów, Czarne Sosnowickie, and Syczyńskie. The concentration of Pb, Cd, and Hg in water, sediment, and freshwater fish muscle tissue was determined, and a food safety assessment was performed. The analysis of water and sediments showed that the sediments were characterised by a significantly higher concentration of heavy metals. Presumably, this ecosystem element plays an important role in the uptake of heavy metal contaminants by fish whose levels were higher in planktonophagous and benthophagous fish species as compared to predatory fish. The food safety assessment showed that amounts of heavy metals in the muscle tissue posed no threat to the health of consumers ingesting that fish species, neither individually (THQ) nor collectively (TTHQ).