The biological and chemical responses, such as the enzymatic activities of isocitrate dehydrogenase (IDH), acetylcholinesterase (AChE) and lactate dehydrogenase (LDH) in the muscle of Chrysichthys nigrodigitatus collected from three trans-urban waterbodies of the Lagos lagoon system: Odo Iya-Alaro, Ibeshe and Agbowa-Ikosi rivers were studied. The sampling sites showed different types and degrees of pollution. The results demonstrated significant differences in muscle activities of IDH and AchE in the Odo Iya Alaro, Ibeshe and Agbowa-Ikosi rivers compared to control fish. LDH activity did not show any difference between sampling sites. Significant correlations were established between some biomarkers and trace metals: AChE was correlated with Pb, Cd and Cu concentrations in water; IDH activity was correlated with Cd and Cu concentrations in water and As, Pb and Cd concentrations in sediments; LDH activity was correlated with As and Zn concentration in water and Cd concentration in sediment. Only one correlation was established between the biomarkers analyzed and the concentrations of PAHs: benzo(b)fluoranthene concentration in sediment and IDH.