The content of total lipids and individual phospholipids was studied in perch Perca fluviatilis L. and ruffe Gymnocephalus cernus L. from two areas of Lake Onego differing in human impact (Petrozavodsk Bay and Povenets Bay). The analysis of hydrochemical data showed that Petrozavodsk Bay is more polluted than Povenets Bay: Lake Onego near the city of Petrozavodsk has a higher (2–3‑fold) content of nutrients and oil products in the water and bottom sediments. The content of total lipids in the liver of perch and ruffe from Petrozavodsk Bay was higher than in Povenets Bay. This is explained by an increase in the share of storage lipids, whose accumulation in the liver indicates a dysfunction of hepatocytes. A decrease in the content of basic phospholipids (phosphatidylcholine and phosphatidylethanolamine) was observed in the liver of perch and ruffe from the lake area at the Petrozavodsk industrial hub. Modifications were detected in some lipid components in the gills of the fish from Petrozavodsk Bay, probably due to the formation of adaptive osmoregulatory mechanisms under exposure to elevated concentrations of organic elements. As opposed to the variation of the lipid indices in nearly all the studied tissues of perch and ruffe from the two areas, the muscle tissue of the fish demonstrated a comparatively low sensitivity to human impact. The comparison scope of the lipid status variation between the fish species showed that differences in biochemical parameters between the areas were more pronounced in perch.