Understanding groundwater salinization and pollution in the arid coastal aquifer is crucial due to complex geochemical processes and sources. This study intends to evaluate the impact of evaporation on groundwater salinity in the arid coastal aquifer, Al Lusub basin, Saudi Arabia using geochemical and multivariate statistical tools. Groundwater samples were collected (n = 52) and analysed for major and minor ions. Groundwater is brackish and shallow wells have higher salinity compared to deeper ones. Hierarchical cluster analysis (HCA) classified the wells into three groups (CG1, CG2, CG3). In these cluster groups, salinity is in the order of CG1(1448 mg/l) < CG2 (3704 mg/l) < CG3(11018 mg/l). PHREEQC modelling reveals that groundwater in this basin is saturated with carbonate, sulphate (CG2, CG3), fluorite (CG3) and silicate minerals, and under-saturated with chloride and hydroxide minerals. Thermodynamic stability diagrams confirm the silicate weathering and kaolinite equilibrium. Precipitation of carbonate minerals at high salinity due to evaporation reduces Ca activity in the groundwater, which triggered the solubility of gypsum and fluorite through common ion effect. Pearson correlation analysis, principal component analysis, ionic ratios (Na/Cl, Cl/Br and F/Cl) and ionic deltas (+ΔBr, +ΔF, +ΔCa, +ΔSO4, +ΔNO3, −ΔNa and −ΔK) justified that non-saline sources and processes, namely evaporation, reverse ion exchange, mineral dissolution and wastewater infiltration predominantly affected the water chemistry in this aquifer. Repeated irrigation practice with high salinity groundwater leads to salt accumulation in the vadose zone due to evaporation, which flushed by the subsequent irrigation events and resulted in higher salinity and NO3− in the groundwater. Hence, sustainable groundwater management and smart irrigation should be implemented.