The spectral analysis of aeromagnetic data over the study area (Northern basement complex, Nigeria) revealed the existence of two major source depths. The second segment of the spectrum layer shows shallow sources ranging in depth from 0.135 km to 0.201 km, with an average depth of 0.140 km. The depth to the basement or deeper source ranges between 1.655 km and 2.021 km, with an average depth of 1.882 km. The Precambrian basement is reflected in the deeper sources, beginning with the first segment of the power spectrum. Structural and topographic relief of the basement surface, lateral differences in basement susceptibilities, and intra-basement features such as faults and fractures contribute to the variation in basement composition. The mean thickness of sediments in the study area is represented by the D2 values obtained from the spectral plots. The depths revealed by this study appears to be reasonable and consistent with previous researchers’ findings. Tectonically active regions have a major impact on heat flows. The average heat flow in thermally normal continental regions is reported to be above 60 mW/m2. Values between 80 and 100 mW/m2 indicate a good geothermal source; values in excess of about 80–100 mW/m2 indicate anomalous geothermal conditions.