The wet season mean concentration of heavy metals were higher than the dry season. Concentration data were processed using Pearson correlation matrix to identify the inter-relationships between physicochemical parameters as well as the sources of heavy metals. The results showed that salinity, pH and temperature among others played a significant role in the adsorption/desorption and dissolution of heavy metals in the surface water. The Enrichment factor (EF) calculated during the wet season in surface water ranged from 0.2 to 2.9 while the EF calculated during the dry season ranged from 0.2 to 1.9. During wet season, Cd, Cu, Fe, Pb and Zn showed minor surface enrichments while Cr and Ni showed no enrichment. During dry season, Cd, Fe and Zn were moderately enriched in surface water while Cr, Cu, Pb and Ni were not enriched. Surface enrichment was attributed to atmospheric deposition, released of sediment bound metals to the surface, dissolution/erosion of coastal sediments as well as anthropogenic input. The computed degree of contamination indicated that the river system was moderately contaminated during dry season but highly contaminated during wet season. The implication is that during flooding which is consequent upon climate change, there will be higher degree of contamination of Qua Iboe River estuary and adjoining creeks.