The Fan Darya is formed at the confluence of the rivers Yaghnob, which flows west from the Yaghnob Valley, and the Iskander Darya, which has its source in Lake Iskanderkul and flows east. Both the Yaghnob and the Iskander Darya drain the valleys between the Zeravshan Range to the north, the Gissar Range to the south and the Fan Mountains to the west. The Fan Darya flows north, crosses the Zeravshan Range and joins the river Zeravshan near the town Ayni.