In an aquatic environment, there is a profound and inverse relationship between environmental quality and disease status of fish. Parasites are one of the most serious limiting factors in aquaculture. Therefore, the present investigation was carried out during the period of February–December 2014 to determine the parasitic infections in the African sharptooth catfish Clarias gariepinus, relative to the capability of internal parasites to accumulate heavy metals. Up to 100 catfish were examined for gastrointestinal helminths and 38% of fish were found to be infected with the cestode Polyonchobothrium clarias. The morphology of this parasite species, based on light and scanning electron microscopy, revealed that the adult worm was characterized by a rectangular scolex measuring 0.43–0.58 (0.49 ± 0.1) mm long and 0.15–0.21 (0.19 ± 0.1) mm wide, with a flat to slightly raised rostellum armed with a crown with two semicircles each bearing 13–15 hooks, followed by immature, mature and gravid proglottids which were about 29–55 (45), 16–30 (24) and 15–39 (28) in number, respectively. The mature proglottid contained a single set of genitalia in which medullary testes measured 0.09–0.13 (0.11 ± 0.01) mm long and 0.05–0.08 (0.06 ± 0.01) mm wide; a bi-lobed ovary was situated near the posterior margin of the proglottid, extending laterally up to the longitudinal excretory canals; the tubular uterus arose from the ootype up to the anterior margin of the proglottid; and vitelline follicles were cortical. The greater portion of the gravid proglottid was occupied by a uterus filled with unoperculate and embryonated eggs. Chemical analysis confirmed that the concentrations of heavy metals (Zn, Cu, Mn, Cd, Ni and Pb) accumulated in P. clarias were higher than in fish tissues and values recommended by FAO/WHO, with the exception of Zn, which was found to be higher in fish kidneys than in the cestode. This supports the hypothesis that cestodes of fish can be regarded as useful bioindicators when evaluating the environmental pollution of aquatic ecosystems by heavy metals.