The Tarago River rises near Gentle Annie Camp, part of the south-eastern portion of the Yarra Ranges within the Bunyip State Park, near Bunyip Gap.

From here the river flows through a series of urban concrete culverts in a south-westerly direction, emptying into the Western Port, southwest of Koo-Wee-Rup.

The river descends approximately 320 metres (1,050 ft) over its 49 kilometres (30 mi) course, prior to entering the Main Drain.

The South Gippsland Highway traverses the Main Drain near its river mouth, emptying into the Western Port.

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