The hydrogeochemical and stable isotopes of water (δD and δ18O) were combined to investigate the deep groundwater recharge processes in the geologically complex intermountain basin (Kathmandu Valley). Results of the stable isotopic composition of the deep groundwater compared with global and local meteoric water lines and d-excess showed the deep groundwater as a meteoric water origin which is insignificantly affected by evaporation. The analysis suggests the deep groundwater was recharged during high rainfall periods (wet season). Additionally, the control of seasonal variation was absent in the deep groundwater and in the spring water samples. The large range of isotopic composition distribution was due to the altitude affect, whereas variations are from the various geological settings of the infiltration encountered during the recharge processes. The tri-linear diagram showed Na-K-HCO3 and Ca-Mg-HCO3 as the two major water types. The distribution of water types in this intermountain basin was found to be unique compared to other basins. Ionic concentration of the samples was found to be higher in the central part than in the periphery due to the ion exchange processes. This study determines the spatial distribution of various recharge processes that depends upon the environment during rainfall and the geological settings.