Seawater intrusion (SWI) is the main threat to fresh groundwater (GW) resources in coastal regions worldwide. Early identification and delineation of such threats can help decision-makers plan for suitable management measures to protect water resources for coastal communities. This study assesses seawater intrusion (SWI) and GW salinization of the shallow and deep coastal aquifers in the Al-Qatif area, in the eastern region of Saudi Arabia. Field hydrogeological and hydrochemical investigations coupled with laboratory-based hydrochemical and isotopic analyses (18O and 2H) were used in this integrated study. Hydrochemical facies diagrams, ionic ratio diagrams, and spatial distribution maps of GW physical and chemical parameters (EC, TDS, Cl−, Br−), and seawater fraction (fsw) were generated to depict the lateral extent of SWI. Hydrochemical facies diagrams were mainly used for GW salinization source identification. The results show that the shallow GW is of brackish and saline types with EC, TDS, Cl−, Br− concentration, and an increasing fsw trend seaward, indicating more influence of SWI on shallow GW wells located close to the shoreline. On the contrary, deep GW shows low fsw and EC, TDS, Cl−, and Br−, indicating less influence of SWI on GW chemistry. Moreover, the shallow GW is enriched in 18O and 2H isotopes compared with the deep GW, which reveals mixing with recent water. In conclusion, the reduction in GW abstraction in the central part of the study area raised the average GW level by three meters. Therefore, to protect the deep GW from SWI and salinity pollution, it is recommended to implement such management practices in the entire region. In addition, continuous monitoring of deep GW is recommended to provide decision-makers with sufficient data to plan for the protection of coastal freshwater resources.