Mapping of the basement relief in regions of a high geological importance is key to mineral prospecting. In this study, we estimate the sediment thickness within the Southern Benue Trough of Nigeria by using synthetic Bouguer gravity data alongside 113 logged borehole data to validate the gravimetric inversion and interpretation. A 3-D gravimetric inversion of the residual gravity data was carried out to determine the thickness of sedimentation after a regional-residual gravity separation. Our numerical results (ranging from 0.8 to 5.5 km) have almost no systematic bias (mean value = 0.045) when compared with the 113 measured sediment depths obtained from drilling profiles. The estimated sediment depths closely mimic the known geological structures and tectonic complexities of the highly rifted Southern Benue Trough of Nigeria. The synthetic Bouguer gravity map exhibits a spatial pattern that indicates possible magmatic movements, which could have led to shallow sediments over and along the Abakaliki Anticlinorium. This elevated crust (because of an upward magmatic movement) created crevices, faults, folds, ridges, or troughs that must have paved way for a thick sedimentary cover that possibly have matured overtime (because of a high temperature) into important habitats for mineral resources. We conclude that the very thick sedimentary cover at the southwestern portion of the study area may have been brought about by a compaction or compression of tectonic plates thereby generating adequate heat and pressure for the maturation of several mineral resources at the Southern Benue Trough of Nigeria.