The Dwyryd rises in the hills to the north of Ffestiniog. At its most northern extent, water draining from Moelwyn Mawr drains into the Tanygrisiau Reservoir, the outflow of which forms the source of the Afon Goedol. This is joined by the Afon Bowydd at grid reference: . Below Rhyd y Sarn, the river is joined by the Afon Cynfal which flows from the east down a deep wooded gorge which includes the spectacular Rhaeadr Cynfal (Cynfal waterfall) south of Ffestiniog. The main river from here on flows through a wide valley formed by glaciation but with a broad flat base formed from re-worked glacial moraines and riverine gravel deposits. The valley, the Vale of Ffestiniog, is worked for agriculture but is subject to routine winter flooding.
Afon Tafarn-Helyg has its confluence about one mile further downstream. This tributary rises south of Gellilydan just north of the Trawsfynydd reservoir but does not receive any water from the reservoir.
There are a number of small lakes and reservoirs in the woodlands north of Plas Tan y Bwlch which also drain south into the river. These lakes include Llyn y Garnedd, Llyn Hafod y Llyn and the beautiful Llyn Mair.
Trawsfynydd reservoir, a large impoundment close to the A470, is the only inland water in the UK that has been used as a source of cooling water for a nuclear power station. The outflow from Trawsfynydd reservoir forms the headwater of the Afon Prysor which flows down another steeply wooded valley before joining the main river at Maentwrog. Large parts of the flow from the reservoir is channelled through the hydro-electric power station at Maentwrog and the flow from the station re-joins the Prysor before the confluence.
As the river moves into a long tidal estuary, it flows under the railway line and under a toll road and rail bridge known as Pont Briwet. Due south of Portmeirion the river is joined by the Afon y Glyn which drains the south west catchment from Llyn Tecwyn Uchaf and Llyn Tecwyn Isaf. The confluence is adjacent to Glastraeth (green beach) - a large extent of salt marsh.
The estuary of the Dwyryd is long and sandy and includes the confluence of the Afon Glaslyn close to the low water mark. The estuary is hauntingly beautiful, though some consider it spoiled by the crossing of National Grid pylons.
The whole of the river drains off igneous and ancient rocks of the Cambrian and Ordovician which are all base-poor. Much of the catchment has also been used for commercial forestry during the last hundred years. As a consequence, many of the tributaries are highly acidic as a result of atmospheric acidification. This has constrained the quality of the fishery and the bio-diversity in many tributaries. Some of these problems have been exacerbated by past industrial actions including metal mining, slate mining, animal skin processing and the use by the army of a gunnery range with large amounts of implaced metal cartridge shells.