Varanasi is an exponentially developing city in the Himalayan-sourced Ganges river basin. To understand the sustainable groundwater-sourced drinking water in Varanasi, it is essential to study the land use-land cover that reflects the surface geomorphology vis-a-vis sub-surface geology, and influence groundwater conditions. We incorporate lithological and groundwater data obtained from an extensive network of boreholes in and around the city at 110 sites, reaching a maximum depth of 100 m below ground level (bgl). The unconsolidated subsurface are primarily composed of sand, silt, clay, and gravel where, silty clay layer. Groundwater quality and stresses were determined through multi-dimensional hydrogeological approaches. The data were analyzed through multivariate statistics (Principal Component Analyses to identify the governing factor influencing the broad hydrogeochemistry. PC1 for urban areas has higher loading values for Fe, Cl− compared to Semi-urban areas highlighting contamination by municipal wastewater. PC2 for urban areas shows higher loading values for Mg2+ and HCO3− compared to semi-urban areas. Due to heavy urbanization in Varanasi, the aquifer suffers substantial groundwater abstraction during particular times of the day compared to the agricultural lands. An increase of about 9% in built-up areas within a span of 10 years (2012–2022) poses a threat to the aquifer system of our study area, jeopardizing access to sustainable drinking water. With the expansion of urbanization and unregulated groundwater extraction, the vulnerability of the aquifer system will probably increase in the foreseeable future. Implementation of sustainable water management policies, engaging all economic sectors of the population in Varanasi, can expedite the process and safeguard the aquifer from attaining its emerging vulnerability. Thus, comprehending evolving groundwater risks through non-invasive methods like that discussed in the present study, holds significant promise for effectively targeting safe groundwater availability in future.