This study analyzed regional magnetic data in the southeastern part of the Niger Delta basin, Nigeria, to delineate deep-seated crustal structures. Enhanced filtering techniques and 3D forward modeling were applied to the magnetic data, revealing the presence of rollover anticlines and faults that act as structural traps in the area. The filtered residual magnetic data indicated geological structures with NE-SW, N-S, and E-W orientations. The study identified faulted crustal blocks, gradient zones, and horst and graben structures with distinct magnetic signatures. The results showed that the sedimentary thickness varied between 4–10 km, while the estimated crustal thickness ranged from 14 to 19 km. This research highlights the effectiveness of magnetic data in mapping basement rock configurations, which play a crucial role in controlling hydrocarbon trapping systems and pathways for hydrothermal mineral accumulation.