This study utilizes geophysical investigations, combining both surface and subsurface methods, assessing quality and mapping aquifers in Haryana’s Mewat district, India. The primary objectives are to delineate the interface between freshwater and saline water, both horizontally and vertically and to perform a quality and sustainability analysis. It has been observed that topsoil, approximately 12 m thick, has resistivity values ranging from 11 to 35 ohm-m, where higher values indicate lower soil saturation. Resistivity exceeding 15 ohm-m correlates with granular zones housing fresh groundwater, while values below 15 ohm-m signal saline to brackish groundwater. Approximately 55% of the region features saline groundwater, mainly in central, western, and southern areas. Freshwater resources within a depth of 30 m cover 26–30% of the area, mainly in the northwest and southwest parts. Beyond 40 m, freshwater availability drops significantly, with depths exceeding 100 m likely encountering hard rock or saline horizons. This study also highlights low freshwater yield challenges due to thin granular zones and variable bedrock depths, some as shallow as 90 m. Additionally, the research examines infiltration rates, ranging from 90 mm/h to 660 mm/h initially and 5 mm/h to 164 mm/h ultimately, with an average rate of 151 mm/h, highlighting sandy soils with some clay limitations. Utilizing available data, a three-dimensional hydrogeological model was constructed, shedding light on groundwater-related issues, such as depletion, waterlogging, water quality, and excess salinity. Groundwater development reached ~80%, categorized as semi-critical. Depletion affects areas with fresh groundwater, and waterlogging is a concern in central and north-eastern regions. In addition to salinity, other water quality issues are higher nitrate, sodium, and chloride concentrations, leading to salt-affected soils in specific blocks like Nuh and Nagina. In summary, this study offers a comprehensive assessment of groundwater resources in Mewat, Haryana, emphasizing sustainable utilization and tailored management of localized challenges. This underscores the importance of integrated water resource management to ensure prudent use while preserving the environment for future generations.