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The overexploitation of coastal aquifers is one of the important reasons for the salinity of groundwater due to seawater intrusion (SWI). This study assesses the hydrochemical changes of the Ghaemshahr-Juybar (GH.-J.) plain. For this purpose, specific statistical methods, modified Piper diagram groundwater quality indicators ([Formula: see text] and [Formula: see text]), groundwater quality index specific to seawater intrusion ([Formula: see text]), and hydrochemical facies evolution diagram (HFE-D) along with GIS (Geographic Information System) techniques were applied to identify the spatiotemporal changes of salinity in coastal multilayer alluvial aquifer. The results show that the chemical composition in the GH.-J. aquifer is basically controlled by three main factors: (1) Caspian SWI and fossil saltwater penetration from an underlying layer, (2) reverse cation exchange process, and (3) feeding by domestic sewage, agricultural activities, and use of nitrate chemical fertilizers. The investigation of the hydrogeochemical facies evolution process shows that due to the reduction of extraction from wells, saltwater infiltration has significantly decreased. Therefore, according to the geological and lithological conditions of the aquifer and exposure to seawater, it is possible to prevent the entry of saltwater from the confined aquifer into the unconfined aquifer and the saltwater intrusion by developing well optimal operation policies in order to control withdrawal from semi-deep wells and the elimination of deep wells. This practical approach to managing the salinity of coastal aquifers is suitable for the allocating groundwater resources and for use in the development of aquifer simulation models., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)