Coastal aquifer monitoring commonly assumes that seawater intrusion decreases progressively with increasing distance from the shoreline. However, this assumption may not hold in hydrogeologically complex coastal settings. This study investigated seawater intrusion in the Paravur coastal aquifer, Kerala, India, using an integrated hydrogeochemical framework to evaluate deviations from the conventional conservative mixing model. A total of 100 groundwater samples were collected along a 9 km coastal–inland transect during the 2025 dry season and analysed using hydrochemical facies, ionic ratios (Cl
–
/Na
+
and Chlorinity Index), the Base Exchange Index (BEX), principal component analysis (PCA), and irrigation suitability indices including Kelly’s Ratio (KR), Magnesium Hazard (MH), Permeability Index (PI), and Residual Sodium Carbonate (RSC).

Although bulk salinity declined substantially inland (mean TDS: 504.61 to 184.06 mg/L from the Core to the Outer Zone), hydrochemical indicators revealed an opposite trend. Na–Cl facies characterised inland groundwater (6–8.7 km), Cl
–
/Na
+
ratios approaching seawater stoichiometry (1.62 ± 0.54 versus 1.81), alkaline pH, and negative BEX values, indicating ongoing salinisation. In contrast, coastal groundwater exhibited mixed sulfate-enriched facies, acidic pH, and positive BEX values, consistent with freshening influenced by anthropogenic contamination. PCA suggested a dual-process control on groundwater chemistry, with PC1 exhibiting strong loadings on Cl
–
, Na
+
, and EC, a loading pattern consistent with salinity gradients influenced by seawater mixing (52.3% of the explained variance). PC2 shows strong BEX loading with Ca
2+
and Mg
2+
, a pattern consistent with cation-exchange (18.8%) processes.

Irrigation suitability assessment revealed a marked freshening–contamination paradox. While 93–100% of samples satisfied the individual criteria for MH, PI, and RSC, 91% of samples exceeded the critical Kelly’s Ratio threshold (KR > 1), with exceedance rates of 100%, 88%, and 76% in the Core, Mid, and Outer zones, respectively, indicating that sodium hazards remained predominant despite declining salinity. These findings suggest that geological heterogeneity and exchange processes may decouple subsurface seawater distribution from surface proximity to the coast, although confirmation of subsurface flow pathways requires geophysical investigation. The study demonstrates that integrating process-based indicators (BEX and ionic ratios) with conventional water-quality indices provides a more reliable assessment of seawater intrusion and hidden sodium hazards than salinity-based monitoring alone. The results highlight the need to extend monitoring networks inland and incorporate hydrogeochemical process indicators into groundwater management strategies for complex coastal aquifer systems.