Commuters are being urged to prepare for more disruption as torrential rain and high winds are expected across much of the country on Thursday.
The worst of the weather is due to arrive during the morning rush hour and the Met Office has issued amber "be prepared" warnings for Strathclyde, Dumfries & Galloway, Stirling, Perth and the southern Highlands.
The heaviest rain is expected to fall in areas that were hit by flooding earlier this week.
More than 100 residents were evacuated from their homes and transport links were cut off in the village of Comrie, Perthshire, after the Water of Ruchill burst its banks.
Properties were also flooded in Dunblane, Aberfoyle, Callander and Dumfries and Galloway. Councils have been distributing sandbags and pumping water from saturated areas during the week to avoid further problems.
The Met Office said southerly galeforce winds will accompany the rain, with gusts of up to 60mph possible in some areas.
Transport minister Keith Brown said: "We have been in regular contact with the Met Office, police, operating companies, the rail industry and other key responders this week.
"Our Multi Agency Response Team will be fully operational to monitor the network and provide assistance.
"I would urge the travelling public and motorists to take extra care in areas that experience testing conditions.
"It looks like a testing rush hour for many people tomorrow and motorists will need to be extra cautious when travelling in heavy downpours and allow extra time for braking distances."