ABSTRACT: Parasitic infections infringe on different organs causing varying degrees of histological changes which contribute directly or indirectly to fish loss. Histological alterations play significant implication in fish health thereby proffer supports for effective diagnoses to improve the management of cultured fish. Various developmental stages of farmed Clarias gariepinus were randomly collected from 100 farms across the three agricultural zones (East, West and Far – East) in Lagos State, Nigeria from purposively classified culture systems based on water usage management systems (WUMS) into daily water renewal (DWR), weekly water renewal (WWR) and bi – weekly water renewal (BWR)). The organs (skin, gills and intestines) were selected for parasitological examinations and histological sectioning using standard procedure. The water qualities monitored were temperature, dissolved oxygen, pH, ammonia, nitrite, iron, alkalinity, hardness and turbidity and measured using standard methods. Descriptive statistics such as frequency count, percentages, standard deviation were used to determine the occurrence and rate of histological changes in relations with parasitic infections while semi-quantitative analysis was used to assess the histological lesion on gills. This study reveals possible relationship between parasitic infections and histological changes on the gills. The protozoans (Trichodina sp, Vorticella sp., Tetrahymena sp., Chilodonella sp., Piscinoodinium sp. and Ichthyobodo sp.) and monogenean trematode (Dactylogyrus sp., and Gyrodactylus sp.) were related parasites found with varying degrees of histological changes like hyperplasia of the epithelial cells, lifting of the primary epithelium, sloughing of the epithelium, fusion of the secondary lamellae, oedema of the lamellae, vacuolation of the epithelial cells, swelling of the epithelial cells, diffuse infiltration of lamina propria by neutrophil and necrosis of the secondary lamellae, classified into stages I, II and III. The most frequently observed histopathology in all the culture systems was hyperplasia of the gill lamellae; DWR-86.96%, WWR – 88.1%, BWR – 92.86%, followed by the fusion of the secondary lamellae; DWR-65.22%, WWR–75%, BWR– 78.57%. No histopathological change was observed on the skin and the intestine and lesions were least in the daily water renewal (DWR) culture system. Hence, it can be safely inferred that good management practice in terms of water renewal system should be encouraged to alleviate parasitic infections and minimize organ damage in cultured fish.