The Met Office has issued Amber "be prepared" warnings for heavy rain in parts of the Highlands & Islands and Grampian regions.
Up to 4ins of rain is expected in the Moray, Speyside and Easter Ross areas in less than 24 hours, which could cause localised flooding and lead to difficult driving conditions.
A Yellow "be aware" warning for rain is in place for the northern and eastern parts of the country.
The Scottish Environment Protection Agency (Sepa) has 12 flood alerts in place.
The Met Office also warned of very windy conditions over parts of northern, eastern and central Scotland, particularly during this morning's rush hour.
Gusts of 50-60mph inland and up to 70mph in some more exposed regions are possible.
Transport Scotland and its partners, including the local authorities, Sepa and Police Scotland, said they are monitoring the situation closely to ensure they are well prepared for the conditions.
Traffic Scotland operator manager Stein Connelly said parts of the North East and Highlands & Islands are likely to face difficult road conditions due to heavy rain.
He said: "We would advise people in these areas to prepare for some travel disruption and to allow extra time for their journeys. They should also check the relevant websites for up to date travel information."
The Met Office said that people should be prepared for some disruption to transport with localised flooding likely.
It said that outdoor activities will also be hazardous due to heavy rain combined with strong winds.
Police in the north, north east and east also warned of possible travel disruption.
Up to 4ins of rain is expected to fall overnight from with the peak likely to be between 5am and 6am today.
Police Scotland said: "There is a possibility of flooding in low-lying land, roads and to rivers which could cause delays to early morning traffic.
"Police are asking that the public allow extra time for travel and if driving, to be aware of possible flooding."