It rises in the Paropamisus Mountains (Selseleh-ye Safīd Kūh) in Ghor Province, flows through the Marghab District in central Afghanistan, then runs northwest towards the Bala Murghab.

[4] The Marghab River originates in the Ghor Province of central Afghanistan, on a plateau among the chain of mountains of Paropamisus, Gharjistan and Band-i Turkestan.

Between Darband-i Kilrekht and Mukhammedkhan, the Marghab crosses the western part of Band-i Turkestan, and then runs toward the northwest in a deep canyon.

The Marghab receives the waters of the Kaysar river on the right, then forms the border between Turkmenistan and Afghanistan over 16-kilometre (10 mi) length.

In Turkmenistan, close to Tagtabazar, the Marghab receives the Kashan River from the left bank, and 25 kilometres (16 mi) further, there is the confluence of the Kushk.