Zimbabwean aquatic systems are threatened by pollution. The objective of the study was to compare the impacts of pollution in Lake Kariba (Sanyati basin) and Lake Chivero. Water samples were collected in June, July and August 2018, while fish were sampled in August 2018. In Lake Kariba, the physicochemical parameters and micronutrients were within acceptable limits, while the organs showed mild histological alterations. The mild histological alterations serve as an early warning sign of the water quality of the Sanyati basin, particularly with the pollutants continuously entering the lake. Poor water quality parameters, such as high phosphorous, ammonia and low dissolved oxygen recorded in Lake Chivero in a higher prevalence of histological alterations in the fish, some of which are irreversible. These observations indicate that Lake Chivero is more impacted than Lake Kariba. In addition, it was noted that most of the histological alterations observed in Lake Chivero are linked to high organic loads. With pollutants continuously pouring into Lake Chivero, the water will soon be unsuitable for a large number of aquatic organisms. Therefore, regular monitoring and the assessment of the lake are strongly recommended to preserve the aquatic biodiversity.