The Met Office issued an "amber" warning of dis-ruption, saying areas hit on Monday were vulnerable to further flooding.
The worst weather is due in Strathclyde, Dumfries and Galloway, Stirling, Perth and the southern Highlands as the conditions move from west to east.
More than 100 residents were evacuated from homes and transport links were cut off in Comrie, Perthshire, earlier this week.
Properties were also flooded in Dunblane, Aberfoyle, Callander and Dumfries and Galloway.
The Met Office said southerly gale-force winds will accompany the rain, with gusts of up to 60mph possible in some areas and 70mph in exposed areas.
Transport Minister Keith Brown said: "Our Multi Agency Response Team will be fully operational to monitor the network and provide assistance."
There are 12 flood alerts, covering Argyll and Bute, Ayrshire and Arran, Dumfries and Galloway, Central, Dundee and Angus, Edinburgh and Lothians, Fife, Scottish Borders, Skye and Lochaber, West Central Scotland, Western Isles and Tayside,