The capital territory of Pakistan constitutes twin cities, Islamabad and Rawalpindi. Islamabad is the capital city, located at the foot of the Margallah Hills, whereas Rawalpindi lies in the Potohar Plateau. Both cities are located in the semi-arid region of Pakistan, where the residents meet their basic need of water through groundwater resources. For the last many years, the quantity and quality of groundwater in these cities has been deteriorating very rapidly. In this study, the foremost recharge source for these cities was identified using tritium and major ion chemistry, and different physiochemical parameters were studied to find out the facts behind the quality deterioration of the groundwater. Tritium values and chemical data suggested that aquifers located in the territory of Islamabad were mainly recharged by upland areas (the Margalla Hills), which accounts for their low electrical conductivity and total dissolved solids contents. A higher sodium adsorption ratio (SAR) suggested an alteration in recharge patterns through soil compaction and cementation (from increased construction activity) that reduced the recharge inputs. The high SAR also disturbs the recharge pattern and had disturbed the natural equilibrium of the groundwater system, deteriorating the quality of the water.