Natural Resources Wales has issued three flood warnings and eight flood alerts for Friday, with adverse weather hitting rail and ferry services.
There are also a number of road closures and drivers have been warned to allow extra time for their journeys.
Network Rail has tweeted that the Macynlleth lines affected by flooding are now open.
A replacement bus service  is being put in place.
The disruption, affecting Arriva Trains Wales journeys between Pwllheli, Aberystwyth and Shrewsbury, is likely to last until 14:00 GMT, the company said.
The Dyfi valley has also been hit by flooding.
Rail passengers are advised to check services before the travel.
The flood warnings have been issued for River Severn at Pool Quay and Trewern, River Severn at Aberbechan, and River Severn at Abermule and Fron.
The A490 in Powys is closed in both directions between A489 at Church Stoke and B4386 at Chirbury due to flooding.
Ferry company Stena Line has said sailings from Holyhead on Anglesey have been delayed and travellers should check departures.
Send us your pictures of flooding in Wales: newsonline.wales@bbc.co.uk
Drivers face travel misery after a night of heavy rain in many parts of Wales.