Bakhtegan Lake, a hypersaline terminal lake in southern Iran, has undergone desiccation due to reduced precipitation, upstream damming, and groundwater overexploitation, posing a saltwater intrusion (SWI) threat to adjacent coastal aquifers. This study presents the first decadal assessment (2010–2020) of SWI in the Khane-Kat Plain, integrating hydrogeological, hydrochemical, and statistical analyses. Water levels from nine observation wells, electrical conductivity from 18 exploitation wells, and major ion concentrations from 15 wells were analyzed using Piper, Durov, Schoeller, Gibbs, HFE diagrams, Pearson correlation, cluster analysis, and PHREEQC-based saturation indices. Results reveal a net water-level decline of 2.14 m (0.21 m/year). Critically, despite stabilization of water levels after 2016, EC and Cl⁻ concentrations continued to increase linearly, confirming that SWI persists independently of the hydraulic head stabilization—a finding challenging conventional management assumptions. Spatial analysis shows marked heterogeneity, with EC values ranging from 1,884 μS/cm (southeast recharge zone) to 16,964 μS/cm (northwest discharge zone), and the aquifer transitioned from three hydrochemical zones (transition, brackish, saline) in 2013 to only two (brackish, saline) in 2020. Strong correlations between EC and Cl⁻ (r = 0.97–0.99), Na⁺ (r = 0.88–0.89), and K⁺ (r = 0.94–0.96) confirm the lake brine as the primary salinity source. All samples are supersaturated with respect to calcite, aragonite, and dolomite, indicating carbonate precipitation risks. These findings necessitate urgent management interventions, including targeted pumping reduction (30–40%), unauthorized well closures, and artificial recharge. This study provides critical evidence that active SWI in arid coastal aquifers requires more than water-level stabilization for effective salinity control.