Located in the Papum Pare district, Naharlagun is situated at the foothills of the Himalayan mountain range. The city is bisected by the Pachin River, a tributary of the Dikrong River, which eventually flows down into the plains of Assam to join the mighty Brahmaputra.
The geography is characterized by dense, sub-tropical broadleaf forests that are exceptionally rich in biodiversity. The flora includes a wide variety of orchids, bamboo, and timber trees. Because it sits at the transition zone between the plains of Assam and the steep mountains of inner Arunachal Pradesh, the environment is intensely green, deeply humid, and defined by the constant presence of moving water.
Natural resources in the immediate vicinity include river boulders, sand, and abundant forest products, though extensive conservation efforts govern their use. The region is seismically active, falling under Seismic Zone V, which shapes local construction and urban planning.

