Heavy rain is expected to hit the north and north-east after a week of scorching weather.
The Met Office has issued a yellow weather warning, which will be in force for 12 hours from midnight on Monday.
All parts of Grampian will be affected, as well as the most south-western parts of the Highlands and the Western Isles.
Persistent heavy rain is expected to batter the regions early on Monday morning before the skies clear out later in the afternoon.
The Met Office has warned residents isolated thunders are also a possibility, with a slight chance of power cuts affecting homes and businesses in some areas.
The warning comes after heavy rain caused travel chaos and landslides in the Highlands earlier this week.
The West Highland Line and the A86 Laggan to Glencoe road were closed on Tuesday due to damage caused by flooding in the area near Roybridge.
Flood alerts issued
Sepa has now issued flood alerts for Aberdeen and Aberdeenshire, as well as Moray, the Western Isles, Skye and Lochaber.
Urban areas and homes located on low-laying ground are at high risk of experiencing flooding tomorrow, with some locations expected to get 3.4ins (80mm) or more of rainfall.
Forecasters are warning transport could also be affected by the adverse weather and drivers should take extra care when out and about.
There could be some cancellations and delays to train and bus services as roads could be impacted by surface flooding.
The Met Office is advising residents in the affected areas to be prepared and expect potential road closures and disruption to travel while the warning is in place.
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