The source of Chagodoshcha lies in the southeast of Leningrad Oblast, south of the town of Pikalyovo.

The river flows in a general southeasterly direction and enters Vologda Oblast, where it accepts the Goryun from the left.

In Vologda Oblast, the Chagodoshcha turns east and accepts the Lid from the left, and, just upstream from the settlement of Chagoda, the Pes from the right.

Both Chagodoshchensky District and its center, the urban-type settlement of Chagoda, are named after the river.

A big portion of the lower course of the Chagodoshcha, downstream of the mouth of the Goryun River, 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.