Motorists have been warned to be extra careful on the roads as torrential downpours are forecast over Thursday and Friday.
Forecasters said there could be almost half the month's average rainfall in these areas over a 48 hour period, with around 80mm possible in some parts.
Sepa has issued 11 flood alerts across the county in areas including Aberdeen and Aberdeenshire, Central and Fife warning residents to be prepared for flooding.
The Met Office has upgraded its existing "yellow" (Be Aware) alert to "amber" (Be Prepared) for Friday in the north east of Scotland and parts of the Aberdeen, Aberdeenshire and Angus areas.
Traffic Scotland is warning of hazardous driving conditions on the A83 between the B828 and A815, at the Rest and Be Thankful. An advisory posted on their website reads: “Increased risk of landslide, drivers and road users must exercise extreme caution when travelling along the road.”
Motorists are asked to expect longer than usual journey times.
The rain will affect most of the country on Thursday evening and is likely to be heaviest across Dumfries and Galloway, Argyll and Bute, Stirling, Perthshire and the southern Highlands, with the potential for localised flooding and travel disruption.
Transport Scotland's multi-agency response team is on stand-by and will be activated if needed.
Transport minister Keith Brown said: "Just weeks after the first major storm of the autumn, the transport network is braced for another major challenge.
"Our operating companies are closely monitoring the situation and are ready to deal with any weather-related issues that arise.
"A wide range of agencies and organisations are poised to react quickly to the alerts and activate their response plans for the potential impact of heavy rain.
"The travelling public also have a key role to play. The Traffic Scotland website, variable message signs and traffic internet radio are being used to provide up-to-date information, allowing them to plan and amend their journeys accordingly."
A "yellow" alert is currently in place for Friday for Orkney, Inverness, Grampian and Tayside.
Marc Becker, hydrology duty manager at the Scottish Environment Protection Agency (Sepa), said: "There is an increasing risk of flooding for north east Scotland on Friday and into Saturday.
"Persistent and heavy rain will move slowly eastwards across Scotland during Thursday, becoming slow-moving across north east Scotland on Friday. This rain may then persist in the north east for a good part of Saturday.
"At the moment, the Met Office has indicated that the heaviest rainfall will be across Aberdeenshire, however other neighbouring areas including Moray, Caithness and Sutherland, Dundee and Angus and parts of Easter Ross could also be at an increased risk of flooding.
"Therefore, we are currently expecting the worst of any flooding impact to be focused in the Aberdeenshire area later on Friday and into Saturday."
He said that Sepa will monitor the situation across the country over the coming days and urged people to remain vigilant and be aware of the conditions if travelling, especially as school holidays begin.
For up-to-date information on road closures and travel disruption visit the Traffic Scotland website.
