The topography of Bongaigaon is generally characterized by flat, alluvial plains formed by the river systems of Lower Assam. Its average elevation is roughly 62 meters above sea level.
While the city itself is relatively flat, the surrounding district features gentle undulations and scattered hillocks. Notable topographical features in the vicinity include the Nakkati Hill, which provides a striking visual contrast to the surrounding plains and offers trekking opportunities. The southern parts of the district gently slope downward toward the massive flood plains of the Brahmaputra River.

