The Gebel EL-Zeit area in the southwestern Gulf of Suez, Egypt, is an area with a significant hydrocarbon potential in sedimentary basins, so that the three-stage inversion method was proposed for the Bouguer anomalies observed therein. Salt diapirs obscured the deep structure of the main central El-Zeit basin; hence, this method was implemented to overcome challenges in 3D seismic modeling. Our study included direct and inverse parameterization sequences that involved analyzing the inputs and outputs within trial-and-error initiations and inverse estimations to assess whether and how much the constraining parameters used in the calculations could achieve the intended aim. Data reduction, filtering, optimization, and constraint assumptions were used to determine the minimal set of density model parameters needed to set limits on the acceptable range of density contrasts that are required to study the basement depths, swells, troughs, faulting/folding and intra-sedimentary structures, and for direct modeling aimed at creating a simple model to save time. The thirteen constrained wells with a total depth ranging from shallow to deep were not involved in direct modeling but provided quality control over the graphical display of the inverse results for the entire study area. Moreover, many parameter constraints were inverted to regulate the way the calculated data are related to the model’s solution that allowed us to determine which inversion trial provided the best parameterization sequence and, therefore, yielded the most appropriate solution for the depth-density model which is approximating reality with a minimal computation error in the study area.