Network Rail Scotland gave an update on the flooding this morning, confirming that the route is open for Avanti West Coast services but that restrictions remained in place.
Trains are unable to pass over the Annan Viaduct.
The line between Dumfries and Carlisle will remain closed until further notice.
A Network Rail Scotland spokesperson said last night: “Two road bridges have been washed away on the river Annan, north of the railway.
"We're unable to allow trains to pass over the Annan Viaduct pending a daylight safety inspection.
"The line between Dumfries and Carlisle will remain closed until further notice.”
In an update they said: We've been working hard throughout the night to deal with flooding which was affecting the West Coast Mainline. The route is open for Avanti West Coast and and freight services, though speed restrictions remain in place.
"At Annan on the Glasgow Central - Carlisle via Dumfries route, the line remains closed until we inspect the Annan Viaduct. Following two nearby bridges being washed away, this requires divers to go into the water. So, until the river flow slows, we're unable to do this.”
The following alterations will remain until at least this afternoon:
Glasgow to Carlisle - Terminates at Dumfries Carlisle to Glasgow - Starts at Dumfries Dumfries to Carlisle – Suspended (replacement transport will be in place)
Four replacement buses are in place. Trains from Glasgow to London will not be affected as they travel on a different route.
Scotrail also announced that due to heavy rain flooding the railway between Wishaw and Lanark the line is closed. Services between Glasgow Central and Lanark have been delayed.
It comes as Residents in Hawick in the Scottish Borders were evacuated as a major incident is declared as the water levels of the River Tweed and River Teviot continue to rapidly rise.
Police Scotland announced that the four were rescued from a premises affected by the flooding on Whitesands in Dumfries.
A Fire and Rescue Service boat was launched to take the individuals to safety and all were safe and well.
Several flood warnings were in place across the region and SEPA issued warnings over the River Teviot in Hawick on Thursday afternoon.