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This study was carried out to assess the heavy metal pollution status and potential ecological risk in the Lagos lagoon, Nigeria. The concentrations of twelve heavy metals commonly associated with environmental pollution were determined in the sediments of the lagoon by Atomic Absorption Spectrophotometry (AAS) and the cold vapor method was employed for Mercury (Hg). Nonempirical risk indices and empirical Sediment Quality Guidelines (SQGs) were used to assess the ecological risk associated with heavy metal in the sediments. The nonempirical risk indices showed that Hg, Arsenic (As), and Cadmium (Cd) are the major contributors to the ecological risk associated with heavy metal pollution in the ecosystem. Comparison of heavy metal concentrations to the Screening Quick Reference Table (SQuiRT) showed that mean concentration of Cd (5.22 and 4.88 mg kg−1in dry and rainy seasons, respectively) exceeds the effect range low (ERL) value (1.20 mg kg−1) in effect to biota. Industries sited around the lagoon have effluent output points in the lagoon serving as a major source of heavy metals coupled with indirect discharges from other sources. Heavy metals are nonbiodegradable, toxic and have the potential to alter ecosystem health, thus pollution sources should be effectively monitored and contained. [ABSTRACT FROM PUBLISHER]