The concentrations of six trace metals (Pb, Zn, Cu, Cr, Ni and Cd) in fish, water and sediment samples from Kubanni River located in Zaria, Northern Nigeria, were investigated. The River receives agricultural runoff and municipal wastewaters, and is utilized for drinking, fishing and irrigation. Some water quality characteristics, the fractionation of trace metals in the River sediments, the risk to water column contamination and the levels of the six trace metals in Clarias gariepinus and Oreochromis niloticus samples were evaluated. Except ammonia (mean 0.72 ± 0.31 mgL-1), all the River water quality characteristics studied were below the recommended drinking water standards by World Health Organization (WHO), the European Union (EU) and Federal Environmental Protection Agency of Nigeria (FEPA). The average values of Pb, Zn, Cu, Cr, Ni and Cd in River Kubanni water were 6.54 ± 1.88, 106.38 ± 14.75, 73.51 ± 11.57, 37.46 ± 6.52, 11.83 ± 3.90 and 0.82 ± 0.37 mg L-1 respectively. These values were below WHO, EU and FEPA limits. Total extractable trace metals from Kubanni River sediments, (Pb, 16.98; Zn, 79.12; Cu, 52.43; Cr, 29.23; Ni, 19.94 and Cd, 4.65 mg Kg-1 dry weight) were all below recommended limits. However, there was considerable risk to River water contamination based on the calculated individual trace metal average contamination factors (IACF) obtained for the River sediments from the trace metal sequential extractions. Also, the distribution and concentration of trace metals obtained in liver, gill, muscle and bone of C. gariepinus and O. niloticus showed that the human health risk for trace metals in muscles of fish were low, but individuals consuming fish livers might be at risk from ingestion of toxic metals at unacceptable concentrations.