It was formed as a meltwater channel for the retreating glaciers at the end of the Ice Age. The Gwaun is a slowly meandering stream passing through marshy, wet woodland with alder trees, water meadows and flood plains. Its river valley is deep and secluded up to where it meets the sea at Lower Fishguard .
It has a total length of 15 km and is navigable with canoes for the lower third of its length, beginning west of Pontfaen. Before Pontfaen, the river is joined by the Afon Cwmau which flows from the south.