The south-eastern part of the Egyptian desert had been waiting for a long time for an exploration process of hydrocarbon potentiality. In this research, we are addressing the available high resolution airborne magnetic data of Delta Wadi Diit area, which were processed and interpreted to map the basement depths and structures as an aid for hydrocarbon potentiality elucidation. Applying a set of automatic interpretation techniques to the magnetic data enabled mapping the tectonic framework of the study area and determining the depth to the basement (in other words, thickness of sedimentary section), which are vital factor of hydrocarbon field analysis. These techniques involve edge detection, depth estimation, as well as 2D and 3D modeling. Edge detection methods include the horizontal tilt angle (TDX) and improved logistic function of total horizontal gradient. Moreover, Euler deconvolution, tilt angle, and source parameter imaging provide both location and depth of the magnetic sources. Interpreted structures reveal that Wadi Diit area is highly affected by shallow and deep-seated faults trending in NW-SE and ENE-WSW and NNE-SSW directions. These fault systems control the surface water drainage network, the contacts of different rock types, the Red Sea rift boundary, and local and reginal basin areas. Depth estimation techniques reveal that the depth of the basement rocks ranges from 300 to 3,500 m for the inshore parts and from 2,500 to 5,000 m for the offshore parts of the area. Basement structure of the area was then refined through applying 2D modeling along two selected profiles and 3D modeling of RTP magnetic data for the entire area. The final depth map reveals major offshore basins at the northeastern side with sedimentary section of more than 3 km thickness. Moreover, local basins are delineated inshore at the southeastern parts. The eastern part of the study area can be considered to be having high hydrocarbon potentialities. Moreover, the inshore basin areas are suitable for groundwater accumulation that makes Wadi Diit delta as one of the most promising areas for sustainable development along the Red Sea’s shore.