Heavy metals and organochlorine residues were determined in water, sediment, fish muscle, and freshwater shrimps from aquatic environments in urban and peri-urban areas in Morogoro, Tanzania. Most of the water samples had heavy metal concentrations below WHO acceptable water quality guidelines. All sediment samples had comparable heavy metal concentrations that suggest natural rather than anthropogenic origin. Hexachlorobenzene, α-hexachlocychlohexane, cis-chlordane, trans-nonachlordane, cis-nonachlordane, pp′-DDE, op′-DDD, pp′-DDD, op′-DDT, and pp′-DDT in hairy river prawn (Macrobrachium rude), African sharptooth catfish (Clarias gariepinus), and Wami tilapia (Oreochromis urolepis) were detected at significant concentrations above the methods' detection limits. The ratio of pp′-DDT to ∑DDTs was 0.4 in O. urolepis and 0.3 in C. gariepinus, which indicated previous rather than current use of DDT. In M. rude, only pp′-DDE was detected and in O. urolepis and C. gariepinus there were higher levels of pp′-DDE than pp′-DDT, which demonstrate uptake of pp′-DDE, rather than pp′-DDT, from the environment. Bioaccumulation of organochlorines and mercury was the highest in C. gariepinus, cadmium in M. rude, and lead in both M. rude and O. urolepis. Maximum detected levels of organochlorine pesticides and heavy metals in M. rude, O. urolepis, and C. gariepinus were below the maximum permissible concentrations recommended by FAO/ WHO. It is concluded that, at present, the contribution of anthropogenic sources in pollution of aquatic environments in Morogoro urban and peri-urban areas are low and that the concentrations of heavy metals and organochlorine pesticides in water and fish do not indicate a risk to the consumers.