High-resolution aeromagnetic data of Nkalagu area, in the southern Benue Trough, Nigeria, were employed for the determination of sediment thickness and characterization of magnetic anomalies in the area for possible mineralization and hydrocarbon prospect. Four methods of depth estimates, namely Euler deconvolution, source parameter imaging (SPI), forward and inverse modeling and radially averaged power spectrum (RAPS), were utilized, and the results were compared. Standard Euler deconvolution for the structural index (SI) of 0.5, 1.0, 2.0 and 3.0 gave depths to magnetic sources that range from 0 to 1500 m, 300 to 3300 m, 0 to 4000 m and 200 to 4200 m, respectively. Depth estimates from source parameter imaging (SPI) range from 135 to 2876 m and spectral depth analysis from RAPS revealed deep and shallow magnetic sources with the shallow source depths ranging from 420 to 850 m, while the depth of deep magnetic sources ranges from 3170 to 5840 km. Four profiles were taken on the total magnetic intensity contoured map and were modeled using forward and inverse modeling techniques. The models suggest the existence of intermediate to basic intrusives at depths between 545 and 1977 m. Generally, it is deduced that pockets of thick sedimentary piles in the area are zones of possible hydrocarbon accumulation. Furthermore, the existence of clusters of straight and curvilinear magnetic lineaments with a predominant NE–SW trend deduced from the tilt derivative grid, reveals four zones of high lineament density which suggest favourable zones for follow-up exploration for base metal mineralization.