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The contamination and potential ecological risk posed by heavy metals from thirteen (13) sediment samples from different sampling sites along the lower portion of Agusan River were analyzed and assessed using different pollution indices. The results obtained shows that the total digest concentrations of different heavy metals under investigation have the following order: Cd < Pb < Zn < Mn, for both first sampling periods. The speciation and distribution pattern have shown that significant amounts of all metals are present in the residual fraction. Similarly, oxide-bound and organic-bound fractions were found to be highly important for Zn and Mn while Cd and Pb were significantly associated in the residual and exchangeable fractions. The results of different pollution indices moreover, showed that among all the heavy metals being studied, Cd posed the highest environmental risk across all sampling stations in both sampling periods and Mn metal was highly enriched and abundant in all of the sampling stations. Importantly, PCA results suggest that Zn, Mn and Pb may have the same origin while Cd might be coming from different sources, and this is corroborated well with the cluster analysis results. The results obtained from this work provide baseline data on the assessment of heavy metal pollution in the lower portion of Agusan River. Importantly, the acquired environmental indices will certainly help safety managers in assessing and interpreting the potential risk of the sediment associated chemical status that might adversely affect aquatic organisms in the selected sampling sites.