The creek originates in Nunawading near Springvale Road, and flows to join the Yarra at the border between Ivanhoe East, Bulleen and Balwyn North.

The poor condition of the creek has been evident from the earliest days of European settlement.

The creek's headwaters meet near the borders of Nunawading and Donvale, 21 km east of Melbourne.

Most settlements are extensions of suburban areas down the Koonung Creek Valley, with Doncaster and Balwyn North being notable exceptions.

The settlements located along its course are listed below, from downstream to upstream; Koonung Creek lends its name to many things, including many local streets and roads;