The climate in the Zerafshan Valley is semi-arid, this is due to the mountains to both the north and south preventing most moist air reaching the area. Rainfall follows an annual pattern with peaks in early winter and spring. From May to October, the weather is dry and calm, providing the valley with ideal conditions for trekking and mountaineering. Winters are usually relatively mild and bring high levels of snowfall. Between January and May, there is a high avalanche risk in the mountains. This can often lead to the closing of the roads north, to Khujand and south, to Dushanbe.
The Zerafshan Valley is an ancient basin, divided by Paleozoic rocks and filled with Meso-Cenozoic deposits.The subsoil is rich in natural resources: very common are deposits of tungsten (in Djilali), antimony, mercury (in Dzhizhikrut, Shing and Magian), and especially coal (in the Fann Mountains and Yagnob). The valley is in fact one of the largest coal deposits of Central Asia. In the valley there are also a Tajik-Chinese gold mine, and a mining and antimony processing plant based in Anzob.