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Regional magnetic data in the southeastern segment of the Nigerian Niger Delta were evaluated with the aim of mapping deep-seated tectonic elements. Enhanced filtering operations and 3D forward modelling were applied on the magnetic data. These geologic features triggered the formation of rollover anticlines and faults that serve as structural traps in the study area. The filtered residual magnetic data revealed geologic structures characterized with NE - SW, N - S, and E - W orientations. The 3-D models detected the faulted crustal blocks, gradient zones, and intra-basement compositional magnetic variations. Furthermore, some prominent horst and graben structures as well as related normal faults characterized with distinct magnetic signatures were observed. Faults of base magnetic (of various compositions) were observed to be the fabricating mechanisms of the magnetic anomalies. Collectively, these structures influenced the patterns of magnetic anomalies with direct effects on the hydrocarbon trapping systems, as well as the pathways and accumulation zones for hydrothermal minerals. On the whole, the interpreted results revealed that the basement surface is rippling. Additionally, the depth result showed sedimentary thicknesses that ranged from 4–10 km. Again, the estimated crustal thickness varied from 14 to 19 km. This study has displayed the capabilities of the magnetic method in mapping the depth and configuration of basement rocks, which are crucial in controlling the formation of structural traps. Identifying these basement structures early helps in understanding the overall geological framework and potential hydrocarbon systems.