The motorway was closed in both directions at the Briton Ferry Bridge, as the storm gathered strength.
On Sunday afternoon, a river burst its banks at Hirwaun, causing the A465 to be closed . Drivers took over an hour to travel between Merthyr and Glynneath, with reports of traffic queuing up to five miles.
Two crashes on the M4 on Sunday afternoon closed lanes at Swansea and Bridgend, with wet weather and high winds making driving conditions difficult.
Winds of 76mph were recorded at the Mumbles.
The A470 was closed in both directions in Powys, as a fallen tree blocked the road. The Cleddau Bridge in Pembrokeshire was also closed to high-sided vehicle.
South Wales Fire and Rescue had a busy day yesterday. This was them helping a homeowner in Cardiff.
How the roads are looking on Monday morning
Storm Freya closed the M4 for a time yesterday and brought flooding to several areas but most roads around Wales this morning are reported clear. There is some heavy traffic in the usual places on the south Wales motorway this morning but no reported trees down or flooding affecting travel this morning.
Tree falls on to dual carriageway in front of drivers
A tree has fallen onto the dual carriageway on the A48 in Cardiff at the Pontprennau junction.
The tree fell right across one lane on the westbound carriageway, reportedly forcing one car to swerve and make an emergency stop.
