Achieving Sustainable Development Goals (SDGs) 6 and 10 requires a comprehensive understanding of the district-level inequality in water and sanitation facilities between rural and urban residences. This study aims to map spatial connections and variations in inadequate access to water and sanitation, as well as the disparities between rural and urban areas in India. We conducted a “quadrant analysis” and Bi-variate LISA mapping to categorize Indian districts based on the level of water-sanitation scarcity and the extent of rural-urban gaps. Our findings reveal a substantial disparity between rural and urban India in the lack of safe latrines (52%), bathrooms (52%), and drainage facilities (45%). Specifically, districts with higher scarcity of safe drinking water sources and greater rural-urban inequality were identified in India's western, central-eastern, and northeastern regions. On the other hand, central-western districts exhibited higher deficiencies in sanitation facilities and wider rural-urban gaps. The outcomes of this study can assist policymakers in prioritizing investments and implementing targeted measures to combat water and sanitation poverty and reduce rural-urban inequality effectively.