The Gwaun rises in the Pembrokeshire Coast National Park on the northern slopes of Foel Eryr in the Preseli Hills, to the east of Pontfaen hamlet.

The river is a slowly meandering stream passing through marshy, wet woodland with alder trees, water meadows and flood plains.

[1] Before Pontfaen, the river is joined by the Afon Cwmau which flows from the south.

The river (as Gwyne) appears on a 1578 parish map of Pembrokeshire.

[2] The river occupies a meltwater channel formed subglacially during the last and earlier ice ages.