Naharlagun features a dynamic, undulating topography. Unlike Itanagar, which is perched higher up on steeper ridges, Naharlagun sits in a relatively lower valley environment at an average elevation of about 200 meters above sea level.
The city is built along the floodplains and lower terraces of the Pachin River. The terrain consists of small hillocks interspersed with narrow valleys. Because of the limited flat land, the city has expanded in a linear fashion along National Highway 415 and up the slopes of the surrounding hills. During the monsoon, the steep hillsides are prone to landslides, and the lower floodplains can experience rapid river swelling.