Stressful environmental conditions are ecological force in modulating adaptive responses of fish populations in aquatic ecosystems with a large number of biochemical and physiological effects associated with increased fluxes of oxyradicals. This study was aimed to examine the impacts of oxidative stress and histological changes in organs of Chrysichthys nigrodigitatus from Ologe and Badagry lagoons. Biomarkers such as biochemical markers [malondialdehyde (MDA) and superoxide dismutase (SOD) and catalase (CAT) and glutathione (GSH)] and histological marker were analysed in C. nigrodigitatus using standard protocols. The biochemical response of C. nigrodigitatus indicated that there was significant increase (p < 0.05) in the activities of MDA and SOD, as well as CAT and GSH in the gill, liver and muscle of the fish samples of both lagoons. The CAT activities in the muscle negatively correlated with MDA in gill (p < 0.05, r = -0.848) in Ologe lagoon. The histological changes in the gill exhibited mild epithelial lifting, fusion of secondary lamellae; inter-lamella hyperplasia, desquamation and necrosis of secondary lamellae. Furthermore, the hepatic tissue showed disseminated moderate microvesicular vacuolation of hepatocytes, moderate vascular congestion and mild presence of eosinophilic fluid within the interstitial. The renal tissue also showed mild hemorrhagic lesion, mild moderate ballooning degeneration of renal tubules and thickened blood vessel. The study provides baseline information that can be useful for effective biomonitoring and future comparative studies of oxidative stress and histomorphological changes in aquatic biota from polluted coastal ecosystems.