Rivers in the Borders, Dumfries and Galloway and Angus were under threat of bursting their banks and there were alerts for parts of the west coast.
On the roads, Dumfries and Galloway was badly affected by fallen trees and localised flooding.
The Erskine Bridge closed to high-sided vehicles on Sunday afternoon. The A78 was shut between Skelmorlie and Largs earlier in the day due to flooding.
A number of people had to be plucked from the water at Dalgety Bay in Fife after a strong gust of wind knocked over a series of dinghies.
Forth Coastguard said no-one had been injured in the incident at about 1200 GMT on Sunday.
The Scottish Environment Protection Agency (Sepa) had two severe flood warnings in place on Sunday evening.
They were for the River Tummel, between Pitlochry Dam and Ballinluig, and the River Tay from Kenmore to the A9 road bridge upstream of Dunkeld.
Ten flood warnings were in force, covering parts of the River Tay, River Lyon, River Earn, River Nith and River Isla.
Kenmore and Loch Tay, the Clyde Coast, the Renfrewshire and Inverclyde coast and the Jed Water were also subject to warnings.
There were also 17 flood alerts covering many parts of the country, from the Highlands to Dumfries and Galloway and the Borders.
The problems came two days after heavy rain caused flooding in Dumfries and Galloway, with the River Nith overflowing in Dumfries.
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