The line from Llandudno Junction, Conwy, and Blaenau Ffestiniog, Gwynedd, was shut after water reached platform level at North Llanrwst station.
In Ceredigion, a tree has been removed from the line between Aberystwyth and Birmingham International after a reported landslip at Llanbadarn.
Network Rail said it was "pulling out the stops" to keep services running.
On Anglesey, speed restrictions remain in place around Gaerwen due to flooding. Network Rail said the situation would be monitored as more heavy rain is forecast for Wednesday.
Wales route managing director, Paul McMahon said: "We're working really hard to keep services running, but unfortunately the Conwy Valley line will be closed for several days with flood waters having reached platform level at North Llanwrst.
"Elsewhere in Wales the impact on services has been relatively limited so far. However, we are monitoring the situation very closely, and with more bad weather predicted it's really important passengers check before they travel, via the National Rail Enquiries website or by calling 03457 48 49 50."
Four flood warnings are in place for north and south west Wales, along with dozens of alerts.
Check if this is affecting your journey

Police were called to the Biffa depot in Avonmouth at 11:00 BST on Friday after being alerted by staff to possible remains at one of the units.
Avon and Somerset Police have named the victim as Matthew Symonds, 34, of no fixed address in Swindon, and said his death was being treated as unexplained.
A post-mortem examination is due to be carried out later.
His next of kin have been informed, police said.
Det Ch Insp Gareth Bevan said officers were "following several lines of inquiry" to establish the circumstances surrounding the man's death.
"Police inquiries so far suggest the body was transported with commercial recycling waste collected in Swindon and therefore the focus of the investigation will be in that area going forward," he said.
"The investigation is at an early stage and we are keeping an open mind about the circumstances leading to this man's death."
Police said it was too early to say how long the body parts had been there.
Biffa is one of the country's leading waste management companies, disposing of rubbish from commercial, industrial and public sector organisations.
Matthew Humphreys, from the company, said: "I can confirm that a body was received at our Avonmouth Transfer Station during the morning of Friday 1st August.
"Biffa takes health and safety very seriously and is conducting its own internal investigation, into the circumstances surrounding the incident."
The Conwy Valley rail route in north Wales could remain closed for several days after heavy rain caused flooding.
[NEXT_CONCEPT]
A man whose body parts were found at a Bristol recycling plant has been identified as a Swindon man by police.