Mineral exploration has gradually shifted from traditional field mapping to integrated geophysical techniques capable of investigating large areas quickly and economically. Hydrothermal mineral deposits are controlled by several geological factors, including faults, fractures, intrusive bodies, hydrothermal alteration, and lithological variations. The Analytical Hierarchy Process (AHP) was employed to delineate the hydrothermal mineralization potential of the Southern Benue Trough, Nigeria, using integrated high-resolution aeromagnetic and airborne radiometric datasets. Advanced geophysical enhancement techniques, like Reduction to the Equator (RTE), First Vertical Derivative (FVD), Analytical Signal (AS), Source Parameter Imaging (SPI), Spectral Analysis, and Centre for Exploration Targeting (CET) grid analysis, were applied to investigate subsurface structures, lithological contacts, intrusive bodies, and basement configurations and depth to magnetic sources. The Analytical Signal map classified the study area into high (>0.0166nT/m), intermediate (0.0093–0.0166 nT/m), and low (<0.0093 nT/m) magnetic zones. High magnetic zones were interpreted as intrusive and structurally disturbed regions associated with hydrothermal activity. SPI depth estimates revealed shallow magnetic source bodies ranging from <0.10 km to >2.7 km, while spectral analysis revealed deeper magnetic source depths ranging from 2.08 km to 9.02 km, with an average depth of 5.01 km. The resulting basement depth model revealed an undulating basement morphology characterized by horsts and grabens that served as depocenters for thick sedimentary accumulations. Structural analysis from the CET grid revealed dominant NE–SW trends with subordinate E–W, WNW–ESE, and NW–SE orientations, reflecting the influence of Pre-Pan-African and Pan-African tectonic events.