More than 30 flood alerts and warnings have been issued for west, central, Tayside and northern regions.
The Scottish Environment Protection Agency (Sepa) said persistent, often heavy, rain and winds were likely to have "significant flooding impacts".
It identified areas around the Spey, Forth and Tay as most at risk.
The warnings are in force from late Sunday to Tuesday. People have also been advised to take care when walking or travelling near coastal areas.
Sepa said this was due to surge, strong winds and wave overtopping, particularly in the Western Isles and Orkney.
Those living and working in the areas affected are advised to plan essential journeys and consider the steps they need to take to be prepared.
Up to date information can be found at Sepa's flood updates webpage.