Abstract The inter-ionic relationships of groundwater present in a region as well as various chemical and physical factors all have an impact on the geochemistry of groundwater in an aquifer. To assess the factors influencing the geochemical composition of groundwater in the eco-sensitive area of Western Ghats, Kerala, India, various weathering, and ionic indices were analyzed. Results show groundwater ranges from soft to extremely hard and acidic to alkaline, with high Mn and Fe levels. WQI analysis found 7% of samples unfit for drinking due to Fe/Mn contamination in the southeast part of the study area. Main water types are CaHCO3 (46%) and CaMgCl. Geochemical modeling indicates silicate and carbonate weathering, cation exchange, and reverse ion processes influence the aquifer. Groundwater is often supersaturated with iron minerals, saturated with carbonate minerals, and undersaturated with sulfate and chloride minerals. Cluster analysis (CA) revealed that NO3 − and K+ are derived from anthropogenic sources. Principal component analysis (PCA) resulted in three factors. Factor 1 is for geogenic processes, while Factors 2 and 3 imply the anthropogenic and weathering of iron-rich minerals. Hierarchical cluster analysis defines anthropogenic input, silicate and carbonate weathering, and different patterns of mineralization in the groundwater. The study underscores the need for comprehensive management to protect groundwater quality, considering the complex interplay of natural processes and human factors.