The towns of Bezhetsk, Pestovo, and Ustyuzhna, and the urban-type settlement of Maksatikha are on the banks of the Mologa River.

The source of the Mologa is in the southeastern part of Maksatikhinsky District, in the eastern outskirts of Valdai Hills.

A stretch of the Mologa forms the border between Maksatikhinsky and Lesnoy Districts.

Downstream of the town of Pestovo, the Mologa turns northeast and enters Vologda Oblast.

The lower course of the Mologa, downstream of the mouth of the Chagodoshcha, belongs to Tikhvinskaya water system, one of the waterways constructed in the early 19th century to connect the river basins of the Volga and the Neva.