The Met Office has issued Amber "be prepared" warnings for heavy rain in parts of the Highlands & Islands and Grampian regions.
Up 100mm 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 Met Office also warned of very windy conditions over parts of northern, eastern and central Scotland, particularly during the Monday morning rush hour.
Gusts of 50-60 mph inland and up to 70 mph in some more exposed regions are possible.
Transport Scotland and its partners, including the local authorities, Scottish Environment Protection Agency (SEPA) and Police Scotland, are monitoring the situation closely to ensure they are well prepared for the conditions.
Traffic Scotland operator manager Stein Connelly said: "The Met Office is telling us that parts of the North East and Highlands & Islands are likely to face difficult road conditions due to heavy rain tonight and into Monday morning.
"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.
"Transport Scotland is in regular contact with The Met Office, Police Scotland and the operating companies and will continue to monitor the conditions throughout tonight and tomorrow."
The Met Office said that members of the public 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.
Marc Becker, hydrology duty manager for SEPA, said: "Wet and windy weather is expected over many parts of Scotland today and into tomorrow which has the potential to result in some localised flooding especially across the east and north of the country.
"We would advise the public to take care during commuting time tomorrow morning in north-east Scotland in particular.
"SEPA will continue to monitor the situation and would encourage the public to check the SEPA website for flood alerts (http://floodline.sepa.org.uk/floodupdates) or call SEPA's flood line on 0345 988 1188 for the most up to date information on their area."
Police in the north, north east and east also warned of possible travel disruption.
Up to 10cm of rain is expected to fall overnight with the peak likely to be between 5am and 6am tomorrow.
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."