The Thomson River rises below Newlands at the north western end of the Baw Baw Plateau of the Great Dividing Range, where it shares a watershed with the Yarra and Tanjil rivers. From its source, the river flows generally north, then east, then south southeast through its impoundment, then southeast, then east, and finally east by south, joined by seventeen tributaries including the Jordan, Aberfeldy, and Macalister rivers, before reaching its confluence with the Latrobe River near Sale. The river descends over its course.