Nubra Valley is located in the northernmost part of Ladakh, sandwiched between the Ladakh Range to the south and the formidable Karakoram Range to the north. The geography is defined by the deep river valleys carved by the Shyok River (a tributary of the Indus) and the Nubra River (which originates from the Siachen Glacier). The two rivers meet near the valley's administrative center, Diskit.
The region is classified as a high-altitude cold desert. Because it sits within the rain shadow of the Himalayas, it receives very little precipitation. Despite the arid conditions, the areas immediately adjacent to the rivers are surprisingly fertile, supporting dense thickets of seabuckthorn, poplar, and willow trees, as well as agricultural plots that contrast vividly with the surrounding barren, scree-covered mountains. The valley forms the gateway to the Siachen Glacier, the longest glacier in the Karakoram and second-longest in the world's non-polar areas.

