Histopatholigical changes were identified in selected target organs from two freshwater fish species, Clarias gariepinus and Oreochromis mossambicus, inhabiting a hyper-eutrophic freshwater aquatic system. The approach was to use a histology-based fish health assessment protocol which included a semi-quantitative histopathological assessment of six target organs (gills, liver, ovaries, testes, kidney, and heart). Results of water quality analysis showed selected variables to be above the recommended levels including pH, ammonia, nitrogen, chloride, and phosphorus. A number of histopathological alterations were identified in the target organs of both species, with the highest number observed in the liver. Species differences were identified in terms of the severity of the alterations within all the organs, with most alterations being regressive in nature. The results of this study provide valuable baseline data for two indicator species inhabiting a hyper-eutrophic system that could be useful for future bio-monitoring studies.