Heavy metal contamination of sediments is a major risk to ecological systems and human health. Not only do sediments influence the quality of the water column, but can be transferred to micro biota and fishes, ultimately ending up at higher trophic levels in the food chain though biomagnification. This study was carried out to assess the contamination levels of heavy metals in the sediments of river Bonsa. Ten sediment samples were taken along the river and analyzed for Copper (Cu), Lead (Pb), Manganese (Mn), Iron (Fe), Zinc (Zn), Cadmium (Cd), Chromium (Cr), Cobalt (Co), and Nickel (Ni) using Atomic Absorption Spectroscopy (AAS). Data analysis was accomplished by comparing the measured heavy metal concentrations to Australian and New Zealand Environment and Conservation Council (ANZECC) and National Oceanic and Atmospheric Administration (NOAA) fresh water sediment quality guidelines and by the computation of geo-accumulation indices and enrichment factors. The results show that apart from Ni which had two of its sample concentrations (at BS1 21.167 mg/kg and at BS2 29.374 mg/kg) exceeding the ANZECC lower limit (21 mg/kg) guideline for fresh water sediment, all other heavy metals recorded concentrations below the lower limits of their respective ANZECC standards. Out of the 10 samples analyzed, 7 recorded Mn concentrations above the NOAA ARC TEL. A one-sample t-test also showed that the mean concentrations of Cu, Pb, Cd, Zn, Ni, and Cr were significantly lower than their respective ANZECC threshold values and Fe concentration was also significantly lower than the NOAA threshold; however, there was no significant difference between Mn mean value and the corresponding NOAA guideline value. The assessment of heavy metal pollution was derived using the Enrichment Factor (EF) and geo-accumulation indices (I-geo).