The transport of heavy metals exponentially binds and infiltrates at varying depths in the Digos River estuarine sediments thereby acting as catchment basin for various pollutants. This descriptivecomparative study aimed to investigate the concentration levels of heavy metals contamination particularly cadmium, chromium, and lead in the three sediment horizons, namely: surface, subsurface and bottom of Digos River estuarine environment and the anthropogenic activities present along the river. Using Flame Atomic Absorption Spectrometer, results showed that the cadmium and chromium concentration levels were found to be significantly higher in the estuarine sediments while lead concentration found to be very low. Moreover, cadmium and chromium concentrations were higher in subsurface sediments compared to the surface and the bottom sediments. Using US EPA/ WHO sediment guidelines to assess the heavy metals contamination in the sediments, it revealed that cadmium and chromium levels had significantly exceeded standard limits. Results proved that there was no significant difference in the level of cadmium and chromium from the different sediment samples. Results showed that the heavy metals contamination in Digos River estuarine sediments may be due to the increasing domestic, commercial, and industrial activities and the use of different agricultural chemicals in Digos City. Hence, a Digos River Education Program was formulated to address this environmental concern.