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The spatial variation of heavy metals (Pb, Zn, Cu, Cd, Ni, Fe) in bottom waters of the Cross River Estuary were examined to understand the effect of anthropogenic pressures on the Estuary eco-system. The average concentrations of heavy metals in water followed the order of Fe>Zn>Ni>Cu>Cd>Pb. The concentrations of Pb, Zn, Cu, Cd, Ni, Fe are low and less likely to have negative effects on aquatic biota. Along channel profile of Cu and Fe demonstrated an increasing distance downstream while Pb and Cd showed an increasing upstream trend. A near uniform distribution was observed for Zn and Ni. Growing industrialization along the Estuary vicinity may lead to enhanced metal concentrations in the water thereby impacting negatively on the eco-system.