Winam Gulf is facing major pollution threats from anthropogenic input of pollutants such as heavy metals and agrochemical residues. This has deleterious effects on flora and fauna in the lake and consequently the quality of omega -3 polyunsaturated fatty acids (PUFAs) which have numerous health benefits in humans. In addition, heavy metal bioaccumulation in fish poses a threat to human health. The major objective of the study was to establish whether there is a correlation between the heavy metal pollutants and the levels of omega -3 PUFAs in fish. Levels of heavy metals -lead, cadmium, Zinc and chromium in sediments, water, and tilapia from selected sites in Winam Gulf were investigated. They were analyzed using Atomic Absorption Spectrophotometer. Fish muscles were further analyzed for omega -3 PUFAs using gas chromatography. Sediment samples accumulated the highest levels of heavy metals ranging from below detection limit to as high as 277 mg/kg on dry weight basis. Zinc levels in fish muscles were the highest whereas cadmium was the lowest. Heavy metal levels in water were found to be lowest compared to sediments and fish. Omega-3 PUFAs, particularly alpha-linolenic, eicosapentaenoic, docosapentaenoic and docosahexaenoic acids were in substantial amounts in fish. Oil contents were in the range of (2.47-3.87) %. There was no clear link observed between the levels of heavy metals and omega-3 PUFAs in fish although the fish muscles showed presence of these metals.