Rifts and rifted passive margins are often associated with thick evaporite layers, which challenge seismic reflection imaging in the subsalt domain. This makes understanding the basin evolution and crustal architecture difficult. An integrative, multidisciplinary workflow has been developed using the exploration well, gravity and magnetics data, together with seismic reflection and refraction data sets to build a comprehensive 3D subsurface model of the Egyptian Red Sea. Using a 2D iterative workflow first, we have constructed cross sections using the available well penetrations and seismic refraction data as preliminary constraints. The 2D forward model uses regional gravity and magnetic data to investigate the regional crustal structure. The final models are refined using enhanced gravity and magnetic data and geologic interpretations. This process reduces uncertainties in basement interpretation and magmatic body identification. Euler depth estimates are used to point out the edges of high-susceptibility bodies. We achieved further refinement by initiating a 3D gravity inversion. The resultant 3D gravity model increases precision in crustal geometries and lateral density variations within the crust and the presalt sediments. Along the Egyptian margin, where data inputs are more robust, basement lows are observed and interpreted as basins. Basement lows correspond with thin crust (), indicating that the evolution of these basins is closely related to the thinning or necking process. In fact, the Egyptian Northern Red Sea is typified by dramatic crustal thinning or necking that is occurring over very short distances of approximately 30 km, very proximal to the present-day coastline. The integrated 2D and 3D modeling reveals the presence of high-density magnetic bodies that are located along the margin. The location of the present-day Zabargad transform fault zone is very well delineated in the computed crustal thickness maps, suggesting that it is associated with thin crust and shallow mantle.