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In arid areas, groundwater quality is an important concern for human life and natural ecosystems. Rapid economic development impacts greatly on limited groundwater resources. This study examines the impacts of natural and anthropogenic contaminations on groundwater quality by integrating hydrochemical investigations, GIS and multivariate geostatistical techniques. Major and trace elements in groundwater were analyzed to evaluate the shallow alluvial aquifer connected to the fractured basement aquifer in the Jazan area of Saudi Arabia (KSA). Results show that the groundwater of the aquifer inland is generally under free conditions and is declining with time, while in the coastal areas, there is a disturbance of the groundwater balance resulting in upward leakage of deep saline water and seawater intrusion. Groundwater types are varied from calcium bicarbonate to sodium chloride, reflecting meteoric water recharge to seawater influence. The pollution risk is high, since the water table is shallow and the aquifers are highly permeable. Urbanization has put stress on groundwater quality due to wastewater contamination from pit latrines and leakage from the unrehabilitated sewage system. Chemical equilibrium and saturation indices were calculated, showing that most of the water samples were under-saturated with respect to anhydrate, aragonite, calcite, dolomite, gypsum and halite mineral phases. This affects carbonate and evaporite minerals in the aquifer, causing ground subsidence and sinkholes in the coastal area. Factor and cluster analyses were used to classify and examine the processes affecting groundwater quality. The main factors impacting on the groundwater hydrochemistry were identified as: dissolution of several minerals, evaporation, human impact, mixing between geothermal and other waters as well as rainfall recharge.