It is an ecotoxicological study aimed at using chemical and bio-monitoring methods to pollution status of the Lower Nun River (LNR) basin using the histo-morphometry of the Liver, Kidney, Gills, and the Testes of Coptodon zillii. Based on literature review on the environmental burdens of the LNR, the following Target Chemicals (TC) were chosen for the study: Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni) and Lead (Pb). The study involved the sampling of water, sediment and feral fish from two stations along the LNR, Peremabiri (PER) and Igbomotoru(IGB) – Experimental sites.Water and sediment samples were analyzed to ascertain the physico-chemical concentrations of potential contaminants, while the harvest fish organs of liver, kidney, gills and testes were subjected to histological study to ascertain the exposure effect. Control fishes were harvested from African Aqua-culture Centre (ARAC) – Reference Site. Analyzed sediment and water values were used to evaluate Environmental Water Quality Index (EWQI) and sediment quality, while the fish organs were analyzes and used for pollution certification and stratification. Study results showed that EWQI of PER was poor (41.9); sediment quality showed that Cr, CU and Pb were above the Maximum Allowable Toxicant Concentration (MATC) for fresh water body. Fish from IGB showed worse lesion prevalence and organ histopathologic Index (Iorg) when compared to PER, with ARAC having the best outcome. The environmental pollution status (EPS) LNR was normal at PER and was slightly polluted at IGB. The study gave credence to the use of histology as a biomarker to assess sublethal effects of environmental stressors, and in determination of the pollution status.