Commuters are being urged to prepare for more disruption as torrential rain and high winds are expected across much of the country.
Amber "be prepared" weather warnings have been issued for Strathclyde, Dumfries & Galloway, Stirling, Perth and the southern Highlands, with the worst of the weather due to arrive during the morning rush hour.
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 gale force winds will accompany the rain, with gusts of up to 60mph possible in some areas.
Transport minister Keith Brown said the government's response team will be monitoring the situation all day. He said: "We have been in regular contact with the Met Office, police, operating companies, the rail industry and other key responders this week. 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 and motorists will need to be extra cautious when travelling in heavy downpours and allow extra time for braking distances. While all of the operating companies and other key agencies involved are working hard to keep Scotland moving and preparations are in place, it's important the travelling public are prepared."
Met Office chief forecaster Bob Wilderspin said: "A particularly squally day is expected as strong to gale force winds combined with heavy rain move across Scotland during the day. With winds gusting around 60mph in places and 20 to 50mm of rain falling in a short period of time we urge everyone to keep up to date with forecasts and warnings, and be prepared for what the weather will bring."
The Scottish Environment Protection Agency (Sepa) has 12 flood alerts in place for Thursday with more expected to be issued throughout the day.
Real-time journey information can be found at www.trafficscotland.org, or on twitter @trafficscotland.