For managing the freshwater in the worldwide coastal aquifers, it is imperative to understand the hydrogeochemical processes and flow patterns in the mixing freshwater/saltwater zone. The Egyptian Nile Delta aquifer is a typical example. The management of seawater intrusion (SWI) requires detailed investigations of the intrusion wedge and the dynamic processes in the mixing zone. Thus, a multidisciplinary approach was applied based on holistic hydrogeochemical, statistical analysis, and DC resistivity measurements to investigate the lateral and vertical changes in groundwater characteristics undergoing salinization stressor. The results of cross plots and ionic deviations of major ions, hydrochemical facies evolution diagram (HFE-D), and seawater mixing index (SMI) were integrated with the resistivity results to show the status of the SWI where the intrusion phase predominates in ~2/3 of the study are (~70 km radius) and the compositional thresholds of Na, Mg, Cl, and SO4 are 600, 145, 1200, and 600 mg/L, respectively, indicating that the wells with higher concentrations than these thresholds are affected by SWI. Moreover, the results demonstrate the efficiency of combining hydrogeochemical facies from heatmap and resistivity investigations to provide a large-scale characterization of natural and anthropogenic activities controlling aquifer salinization to support decision-makers for the long-term management of coastal groundwater.