Services have returned to normal between Prestatyn and Chester after 'an operating incident'.
Normal service has resumed on Arriva Trains Wales between Pembrey and Burry Port and Llanelli.
Trains are also now stopping as usual on Arriva Trains Wales at Pembrey and Burry Port after emergency services dealt with an incident.
There are delays of up to one hour on Arriva Trains Wales services between Carmarthen and Manchester Piccadilly, between Carmarthen and Llandovery and between Pembroke Dock and Swansea.
There's replacement bus service running on Great Western Railway between Carmarthen and Swansea.
Emergency services are dealing with an incident between Carmarthen and Llanelli.
National Rail says the disruption to services is expected until 8.30am
Passengers are being urged to check before they travel between Newport and Shrewsbury as Network Rail embarks on upgrade works over six consecutive weekends beginning on 11 June.
Network Rail says there will be significant work at Shrewsbury station and signalling upgrade work in and around Hereford station. The work finishes on Sunday, 17 July.
Bus replacement services will be running during work between Newport and Shrewsbury, with the exception of Saturday, 9 July when trains will be running between Newport and Hereford because of the World Speedway Championships at the Principality Stadium in Cardiff.
Arriva Trains Wales says it's extending its mobile ticketing system across the country after a successful trial on the Cardiff and Valleys network.
It says customers can make savings using Mobile Multi-flex ticket - the first mobile ticketing system of its kind in the UK.
Tickets can be bought, through an app, to travel between any two places and can be stored on a smartphone for up to three months after the date of purchase.
A signalling problem at Abercynon means trains are unable to run between Pontypridd and Aberdare / Merthyr Tydfil.
Buses will replace trains between these stations, extending journey times by up to 30 minutes.
This is expected to last until 07:30.
There are possible delays on Arriva Trains Wales at Betws-y-Coed because of sheep on the line.
Arriva Trains Wales says, from today, it's tripling the number of services from North Wales to Manchester Airport.
It means there will be 57 services a week.
The company says Manchester Airport is already an extremely popular airport for Welsh travellers with more Welsh residents flying from Manchester than any other airport – including Heathrow.
There are delays on Arriva Trains Wales between Criccieth and Porthmadog because of a problem with lineside equipment.
There are delays of around 15 minutes on Arriva Trains Wales between Treherbert and Pontypridd because of signalling problems.