Up to four inches of rain was expected in the Moray, Speyside and Easter Ross areas over a 24-hour period from last night.
Localised flooding and difficult driving conditions were predicted for this morning's peak traffic hours. Outside of this time, a yellow "be aware" warning for rain is in place for northern and eastern parts of the country.
A yellow warning has also been issued for strong winds moving from the north of England overnight up the east coast of Scotland, with gusts of up to 40mph.
Transport Scotland and partners, including the local authorities, Scottish Environment Protection Agency (SEPA) and Police Scotland, are closely monitoring the situation.
Traffic Scotland operator manager Stein Connelly said: "The Met Office is telling us that parts of the North East and Highlands and Islands are likely to face difficult road conditions due to heavy rain on Sunday night 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 and Police Scotland and the operating companies will continue to monitor the conditions"
Marc Becker, hydrology duty manager for SEPA, said: "Wet and windy weather is expected over many parts of Scotland, 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 [on Monday] morning in north-east Scotland in particular."
Rachael Vince, a forecaster with MeteoGroup, said after the heatwave that saw parts of Scotland bask in temperatures of around 27C, this week was more "typical British summer. A bit of rain in August is nothing unusual. We are in for an unsettled spell."
Organisers had to postpone the prestigious Sevenstar Round Britain and Ireland Race, which was due to kick off from the Isle of Wight yesterday, after severe storms.