Mountainous catchments are one of the world’s important water sources that sustains a major portion of global population and a rich biodiversity. The groundwater quantity and quality of mountainous watersheds depend generally on the geologic characteristics and climate gradients. Although many groundwater studies have been carried out in the midlands and lowlands of many river basins, not enough focus has been paid to the mountainous catchments of tropical watersheds. Here we report a case study on groundwater quality and controlling factors of a mountainous catchments of the Western Ghats mountain ranges of peninsular India—the Bhavani river basin, which is identified as a testbed for long-term monitoring of the Critical Zone process. A total of 88 water samples were collected seasonally for assessing various physico-chemical parameters, solute contents and scaling properties. Standard methods were followed for the estimation of various hydrochemical parameters in the open and borewell samples. The results of the study revealed that higher pH and Total Dissolved Solids (TDS) are noticed in the talc-tremolite dominated central zone whereas low values are recorded in the charnockite dominated areas. The major cations in the water samples are of the order Ca2+ > Mg2+ > Na+ > K+ and the anions are of the order HCO3− > Cl− > SO42−. The content of Cl− shows higher values in areas close to agricultural/settlement areas. An overall evaluation shows that the hydrochemistry of groundwater in the study area is influenced by both silicate and carbonate weathering. Mineral stability indices computed for the groundwater reveal that about 52% of the samples are supersaturated with carbonate minerals and often exhibit scaling due to solute overloading. Saturation Index and mineral stability diagram also support that the incongruent dissolution of aluminosilicate minerals (silicate weathering) is an important hydrochemical process controlling the chemistry of groundwater. Langelier saturation index (LSI) and Puckorius scaling index (PSI) show that a significant number of open well and borewell samples exhibit scaling tendency. Among the contributing factors that determine water quality of groundwaters, chemical weathering and anthropogenic activities play a significant role.