Located in western Assam, Bongaigaon sits on the northern banks of the Brahmaputra River valley. The city is nestled in a predominantly flat plain, characterized by the lush, fertile soils typical of the Brahmaputra basin.
The region is crisscrossed by several smaller rivers and tributaries, most notably the Aie River, which flows down from the Bhutan hills. Bongaigaon's geography forms a natural gateway to the forested hills of western Assam and neighboring Bhutan, creating a landscape that is both agriculturally rich and ecologically diverse. Dense foliage, wetlands, and small lakes (beels) are common in the periphery of the urban center.