This study applied a nuclear technique in conjunction with a classical monitoring tool to characterize the origin, fate, and behavior of metal pollutants in groundwater of Islamabad-Rawalpindi Metropolitans, which are also known as the “twin cities.” In total, 122 groundwater samples were collected and analyzed in accordance with standard methods. GIS and multivariate statistical analysis were employed for the groundwater vulnerability assessment and source apportionment. The results of the aesthetic parameters indicated that the majority of groundwater sources were tested and were colorless, odorless and tasteless in the “twin cities.” In addition, the findings of this study indicated that the concentration of pH, phosphates, copper, manganese, and zinc were within the drinking water standards in the “twin cities” as stipulated by the World Health Organization (WHO) and Pakistan Standard and Quality Control Authority (PSQCA) at all sampling points in the study area. The groundwater quality was found unsuitable for consumption due to elevated levels of electrical conductivity and total dissolved solids at 9.83% and 4.09% of samples, respectively. The contents of arsenic and fluoride were well within the allowable range at almost all points except at one location. However, iron and lead contents were above permissible limits. A statistical analysis revealed that trace metals originated from both geogenic and anthropogenic sources such as enhanced rock-water interaction, over abstraction, evaporation enrichment, improper waste disposal, discarded batteries, cross contamination of water supply and sewerage lines, active recharge from Lie drain, and domestic, industrial, and agricultural effluents. The computed water quality index (WQI) based on heavy metals elucidated that groundwater quality was poor in most of the study area due to elevated electrical conductivity, total dissolved solids, lead, iron, arsenic, and fluoride values. A highly depleted isotopic composition of 13C provides clues about the aquifer’s vulnerability from miscellaneous sources such as domestic, urban, construction, and agricultural sites and the dissolution of carbonate minerals. This study clearly indicates that a rapidly growing population, unplanned urbanization, industrialization, improper waste disposal, over abstraction, and a lack of water abstraction policies are significantly contributing toward the impairment of groundwater quality in the study area. The study strongly emphasized the need to regulate groundwater abstraction by improving water treatment and the supply system for the provision of safe water to the urban populace. These results will help in designing remedial strategies for improving water quality in the “twin cities.”