The Kunduz rises in the glacier region on the north side of the Koh-i-Baba range in Bamiyan Province, some 20 km south west of the town of Bamiyan, where the river is known as the Bamiyan River. It flows east in a deep valley separating the western part of the Hindu Kush on the north from the Koh-i-Baba on the south. After about 50 km it bends sharp north, crossing the Hindu Kush range. It then turns east-north-east and enters Baghlan Province. There the river is known as the Surkhab.
It then parallels a northern spur of the Hindu Kush for more than 80 km, receiving many small tributaries on its right bank.
The basin of the Kunduz River covers almost all the province of Baghlan, the western part of Bamiyan Province and two-thirds of Takhar and Kunduz Provinces. Its area is estimated at 31,300 square kilometers.
At Pol-e Khomri, annual mean flow was 67.6 m³ per second, from a basin of 17,250 square kilometres.