Nongstoin is located in the western part of the Meghalaya plateau, a region characterized by ancient, hard rock formations and lush greenery. The geography is dominated by undulating hills, deep gorges, and dense subtropical pine forests.
The area is intersected by several important rivers and streams, most notably the Kynshi River, which gives life to the region's famous river islands and waterfalls. The broader West Khasi Hills district surrounding Nongstoin is also known for rich mineral deposits, including coal, sillimanite, and significant reserves of uranium in nearby areas like Domiasiat, though large-scale mining remains a sensitive and heavily debated environmental issue.

