Various physico-chemical parameters, including fluoride (F−), were analyzed to understand the hydro-geochemistry of an aquifer in a semi-arid region of India. Furthermore, the quality of the shallow and deep aquifer (using tube well and hand pumps) was also investigated for their best ecological use including drinking, domestic, agricultural and other activities. Different multivariate techniques were applied to understand the groundwater chemistry of the aquifer. Findings of the correlation matrix were strengthened by the factor analysis, and this shows that salinity is mainly caused by magnesium salts as compared to calcium salts in the aquifer. The problem of salinization seems mainly compounded by the contamination of the shallow aquifers by the recharging water. High factor loading of total alkalinity and bicarbonates indicates that total alkalinity was mainly due to carbonates and bicarbonates of sodium. The concentration of F− was found more in the deep aquifer than the shallow aquifer. Further, only a few groundwater samples lie below the permissible limit of F−, and this indicates a risk of dental caries in the populace of the study area. The present study indicates that regular monitoring of groundwater is an important step to avoid human health risks and to assess its quality for various ecological purposes.