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The present study reports the bioaccumulation of cadmium (Cd), zinc (Zn), lead (Pb) and mercury (Hg) in the gills, muscles and intestine of Tilapia zillii, Malapterurus electricus and Clarias gariepinus sampled from fishermen at Niger River, Onitsha shelf. Heavy metals in gills, muscles and intestine of fishes was investigated using Varian AA240 Atomic Absorption Spectrophotometer. Mean cadmium concentration in the fish organs was highest (0.068 ± 0.02 mg/kg) in the gills and lowest (0.040 ± 0.01 mg/kg) in the muscles. The descending order of mean cadmium concentration in the organs is gills > intestine > muscles. T. zillii and C. gariepinus had the maximum and minimum mean cadmium concentration of 0.087 ± 0.04 mg/kg and 0.043 ± 0.01 mg/kg, respectively. Cadmium concentration in the fish organs were lower than the FAO/WHO standard for seafood, thus the fishes with this levels of heavy metals are safe for human consumption. The mean concentration of zinc in the organs of the studied fish species was highest (8.180 ± 3.508 mg/kg) in intestine and lowest (4.176 ± 1.091 mg/ kg) in the muscles. The descending order was intestine > gills > muscles. Mean zinc concentration was maximum (8.848 ± 3.39 mg/kg) in T. zillii and minimum (5.084 ± 1.17 mg/kg) in M. electricus. These values were below the FAO/WHO recommended standard limit of zinc (10–20 mg/kg) in fish samples. Lead and mercury were not detected in any of the fish. The result obtained in this study, revealed that Niger River is contaminated to varying levels by zinc and cadmium. Control measures recommended include public enlightenment on the need to desist from anthropogenic activities that could lead to water pollution.