This study examined the ecotoxicological evaluation of commercial fish pond in Mgbuoba, Port Harcourt, Rivers State Nigeria using water quality and gross anatomical assessment of Clarias gariepenus, using African Aquaculture Centre (ARAC) as a reference site. In this research the following were done: Gross anatomical assessment of the farmed fish which comprised of condition factor (CF), Organo-Somatic Index (OSI) and Health Assessment Index (HAI) and physico-chemical properties of pond water. The chemical assessment involved environmental water quality index (EWQI) and heavy metal assessment. The gross anatomical assessment involved the sampling of twenty table-sized fish harvested from the Mgbuoba commercial fish pond which were compared with ten table-sized fishes of the same specie harvested from an aqua-cultured centre, ARAC. The EWQI of the commercial fish pond was considered to be of a fair quality, condition factor recorded showed that fishes from Mgbuoba were in better condition than that of ARAC, health assessment index was poor in fishes harvested from ARAC. The organosomatic index showed that Mgbuoba fishes had a high mean values for Gills and Liver respectively. Using one-way Anova statistical analysis, no significant difference (p>0.05) were noted between Mgbuoba commercial fish pond and ARAC. It is suggested that at intervals the health status and water control should be examined/analyzed to keep a suitable habitat for the fishes and make consumption safe humans.