The phenomenon of seawater intrusion is becoming increasingly problematic, particularly in low-lying coastal regions and areas that rely heavily on aquifers for their freshwater supply. It is, therefore, vital to address the causes and consequences of this phenomenon in order to ensure the security of water resources and the sustainable use of water. The objective of this paper was twofold: firstly, to delineate zones with different salinization levels over time; secondly, to investigate the factors controlling seawater intrusion of the Nile Delta aquifer. Aquifer data were collected in Sharkia governorate, Egypt, over three historical periods of years: 1996, 2007, and 2018. The dataset used to create the linear model of coregionalization consisted of hydrogeological (water level), hydrodynamic (pH, EC, Na, Mg, K, Ca, HCO3, SO4), and auxiliary (distances from salt and freshwater sources) variables. Cokriging was applied to produce spatial thematic maps of the studied variables for the three years of the survey. In addition, factorial cokriging was applied to understand the processes beyond the change in the aquifer water quality and map the zones with similar characteristics. Results of mapping the first factor at long range over the three years indicated that there was an increase in seawater intrusion, especially in the northeastern part of the study area. The main cause of aquifer salinization over time was the depletion of the groundwater resource due to overexploitation.