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Lake Victoria is an important source of fish for domestic, regional and global market. Recently, the lake has experienced severe pollution from wastewater and industry. Winam Gulf, located on the eastern side of Lake Victoria Kenya is currently under pollution threat from multiclass pollutants including heavy metals, potentially harming human health and aquatic biodiversity. Therefore, the objective of this paper was to investigate the comparative analysis of heavy metal loading from sewage effluents and Inlet Rivers in the Winam Gulf of Lake Victoria, Kenya using appropriate standard methods. Data obtained show that Nickel average concentration 0.255 mg/l exceeding 0.07mg/l WHO acceptable standards; Lead average concentration 0.048 mg/l exceeding 0.01 mg/l WHO acceptable standard; Cadmium average concentration 0.037mg/l exceeding 0.003mg/l WHO acceptable standard. Among the rivers sampled, River Kisat showed higher concentrations of all the heavy metals analyzed than River Nyando. Heavy metal concentration of the sediment and water samples collected from the different sites were significantly different (p≤0.05). In conclusion, the concentrations of Nickel, Lead, and Cadmium in water samples exceeded WHO standards, especially in River Kisat. The study recommends that there is need to conduct routine assessment of the levels of heavy metals within the gulf, stricter enforcement of regulations governing waste water treatment and discharge and improved efficiency of wastewater treatment plants.