There is need for the investigation into heavy metals and microbial loads in edible aquatic organisms, to evaluate their safety and compliance with standards approved by international regulatory bodies’ which regulates food and water quality. The heavy metals and total heterotrophic bacterial (THB) concentrations in catfish, surface water bodies and sediments collected from the wetlands of Isoko region of Delta State, Nigeria were determined in accordance to standard approved methods. The laboratory results revealed that the lead, cadmium, zinc and THB concentrations in the fish body parts (gills and muscle) sampled were lower, compared with those obtained from sediments samples. The lead concentration was 1.13 mg/kg and 28.01 mg/kg for the water and sediment samples respectively. Cadmium concentration of 0.19 mg/kg and 1.64 mg/kg was recorded for the water and sediment samples respectively. Then the zinc concentration was 0.39 mg/kg in the water sample and 87.17 mg/kg in the sediment samples. In terms of the fish body parts, the results revealed that the zinc, lead, cadmium and THB concentrations in the fish gills were higher, compared to the values recorded in the fish muscle. It was observed that the cadmium concentration in the fish gills and muscle was higher than the maximum allowable limit of 0.17 mg/kg approved by the FAO; while the lead and zinc concentrations in the fish gills and muscle were lower than the maximum allowable limit of 0.5 mg/kg and 67.1 mg/kg respectively, approved by the FAO for edible fish. Finding from this study will be helpful in taking appropriate measures to prevent bioaccumulation of toxic heavy metals and microbes in aquatic organisms, to levels above the maximum allowable limits approved by FAO or other regulatory bodies.