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Abstract Groundwater depletion is an emerging problem worldwide due to changes in climate and an increase in urbanization. Two significant water-bearing formations, the Oligocene-aged Nari and the Miocene-aged Gaj, were utilized as a case study exposed near Karachi, Pakistan. Groundwater budgeting was performed through a classical equation. The inflow of groundwater in the formations was calculated by thermo-pluviometric data and water loss of Hub Dam. The potential of evapotranspiration (PET) was calculated by the Thornthwaite method. The groundwater inflow from Hub Dam was estimated by using 20 years of annual water loss data by removing PET. The total mean annual inflow of groundwater in the formations was 2414.12 US Gallons per Second (gps). The annual mean outflow was estimated by calculation of groundwater usage for industries and domestic purposes and the mean annual groundwater outflow was 5562.61 US gps and an annual deficit of groundwater was 3148.5 US gps. The research is composed of validating the groundwater budget. Direct Current Electrical Resistivity (DCER) and static water level data from existing industrial wells were used for groundwater maps. The DCER data indicates A-Type and K-Type sub-surface with high resistivity in the three-layer model. The average water table of residential areas in 2019 was 60 m and in industrial areas was 130 m. The oscillation of the groundwater table over the last 20 years and the deficit of the groundwater budget shows an alarming condition for the future. If the same scenario persists, then by 2025, the water table will decline up to 140 m.