The present study deals with the hydrogeochemistry and water quality of shallow aquifers in two important river basins—the Ithikkara and Kallada river basins—draining the south western flanks of Western Ghats in Kerala, South West India. Well water samples were collected from 20 dug wells with a depth range of 1 m below ground level (mbgl) to 18.2 mbgl during pre-monsoon, monsoon, and post-monsoon seasons of the year 2011–2012. These samples were analyzed for various physico-chemical parameters following standard methods and were evaluated for their interrelations and drinking water suitability. The pH of the water samples shows wide variation from highly acidic to highly alkaline water. About 80% of pre-monsoon samples recorded Fe2+ concentration above the permissible limit of drinking water standard. Water Quality Index (WQI) shows that majority of the well water samples fall in the category of excellent–good for drinking purpose. The results of the irrigation suitability assessment using the procedures like Percent Sodium, Sodium Absorption Ratio, Residual Sodium Carbonate, Kelly Index, Permeability Index, and Magnesium Hazard reveal that the well waters of the study area are fit for irrigation purpose. Na+/Cl− ratio reflects the release of sodium to water due to silicate weathering. The samples have a Ca2+/Mg2+ ratio equal or greater than 2 indicating the effect of silicate minerals in contributing Ca2+ and Mg2+ ions to the well water. The saturation indices reveal that groundwater is supersaturated with SiO2. Among the causative factors that determine the hydrochemical quality of well water samples, silicate weathering plays a pivotal role with significant input of ions from anthropogenic sources.