The Kubena is the principal tributary of Lake Kubenskoye and belongs to the basins of the Sukhona and the White Sea.

The river basin of the Kubena comprises vast areas in the center of Vologda Oblast and in the south of Arkhangelsk oblast and separates the river basins of the Onega in the west and the Vaga in the east.

Four district centers of Vologda Oblast, Syamzha, Kharovsk, and Ustye, are located in the basin of the Kubena.

Downstream of the town of Kharovsk the Kubena accepts the Sit from the right and eventually turns southwest.

Further the Kubena enters Ust-Kubinsky district and empties into Lake Kubenskoye, forming a river delta.