Groundwater samples were collected from 44 wells in the Ramganga Sub-Basin (RSB), India, and analysed for major ions, nutrients and trace metals. The primary goal of this study is to evaluate the hydrochemistry and to identify the geochemical processes that govern the water chemistry in the shallow and deep tube wells in the study area using geochemical methods. The knowledge of changes in hydrochemistry of the aquifers is important for both groundwater recharge and use in the region. This study found that there are substantial differences of water chemistry between shallow and deep wells. In the shallow wells, the average concentrations of total dissolved solid (TDS), Na, K, Ca, Mg, HCO, Cl, SO, NO, PO, F, Cu, Mn, Fe and Cr are twofold higher than the deep wells. The concentrations of dissolved silica in the groundwater do not vary with the depth, which implies that the variation in the water chemistry is not due to mineral dissolution alone. Major ion ratios and saturation indices suggest that the water chemistry is predominantly controlled by dissolution of carbonate minerals, silicate weathering and ion exchange reactions. Thermodynamic evaluation (ion activity ratios and stability filed diagrams) indicates that the kaolinite and gibbsite controlled the water chemistry in the both shallow and deep wells. In addition, the groundwater chemistry in the shallow wells is affected by the vertical infiltration of contaminated water from surface contamination sources and nitrification process. In the deep wells, absence of NO and low concentrations of Cl, SO, PO and F imply the role of regional flow and denitrification in the groundwater. Results concluded that proper management plan is necessary to protect the shallow aquifer in the RSB since shallow aquifer pumping is less expensive than the deeper one.