The Met Office has issued an amber "be prepared" alert for Grampian, the Borders, Lothians, Central, Tayside and Fife into this morning, while the Scottish Environment Protection Agency (Sepa) has issued nine flood alerts across the country.
A Met Office spokesman said the north-east of Scotland would be the worst affected today with heavy rain.
Drivers are again being advised to take care and reduce their speed as surface water is likely to make conditions more difficult.
The Scottish Government said the Multi Agency Response Team will be running until the weather improves.
Forecaster Andy Ratcliffe, of MeteoGroup, said further rain was expected throughout the day following persistent rain overnight.
Marc Becker, from Sepa, said: "Into Wednesday it will be wet across most of eastern and southern Scotland, including the central belt, with the heaviest rain expected in the east of Scotland from the Borders up to parts of Angus.
"We are working closely with the Met Office to get a better picture of the potential flooding impact as a result of this heavy rain."
Eastern Scotland has already been hit with winds up to 75mph, while gusts in the west reached 55mph.
The Borders suffered some of the worst weather yesterday, with up to 2.5 inches of rain on already saturated ground.
Scottish Borders Council activated its emergency response team in expectation of "the equivalent of an average month's rainfall in a day".
Transport minister Keith Brown said: "In light of the Met Office warning for wind and rain in many parts of the country, our trunk road operating companies have all their resources available, including patrols, and will pre-position resources in areas of special attention."
Tayside Police also called for motorists to drive with "utmost care" in light of the weather conditions.
A spokesman said: "Anyone who is travelling should allow plenty of time for their journey, reduce their speed and drive according to the conditions."