<p>Groundwater degradation poses a critical threat to water security in the Indian subcontinent, driven by intensifying anthropogenic pressures and geogenic processes. This study conducts a comprehensive comparative assessment of spatial groundwater quality dynamics between the agriculturally intensive Ganga River Basin (GRB) and the ecologically distinct Brahmaputra River Basin (BRB). Utilizing 2325 samples from the Central Groundwater Board (2018), the analysis integrated the Water Quality Index (WQI), Inverse Distance Weighting (IDW), and Welch’s t-test across 12 key parameters (pH, EC, TH, Calcium, Mg, Cl, Bicarbonate, Sulphate, NO₃, Fluoride, and Na). Results reveal profound, statistically significant disparities: the GRB faces widespread degradation, with 14.62% of samples deemed ‘unsuitable’ for drinking, primarily driven by intensive agriculture (63.43% land use), high population density, and geogenic fluoride. Conversely, the BRB exhibits superior quality, with 48.44% of samples classified as ‘excellent,’ attributed to extensive vegetation cover (61.33%) acting as a natural filter and dynamic hydrological flushing. The study highlights the critical role of land-use patterns in determining water quality, demonstrating that natural vegetation buffers against contamination significantly better than agricultural zones. Consequently, differentiated management strategies are essential: urgent remediation and regulation of agrochemicals for the GRB, and proactive conservation for the BRB. These findings provide a scientific roadmap for ensuring sustainable water management, directly contributing to the realisation of Sustainable Development Goals 6 (Clean Water and Sanitation) and 3 (Good Health and Well-being).</p>