The Scottish Environment Protection Agency says river levels throughout the region are falling but are expected to rise again on Saturday because of further rain.
The flood alert is primarily focussed in the west of the region. Surface water may also occur during heavier periods of rain but these are expected to be localised and minor.
An amber flood alert has been issued for Dumfries and Galloway.
Melting snow and heavy rainfall have caused the River Esk and River Nith to rise, which may cause some localised flooding.
A flood alert has been issued for the River Eden in Cumbria due to a forecast of heavy rain from midnight until noon tomorrow (29th December 2012).
The alert covers Upper River Eden, through the Eden Valley, Warwick Bridge, Crosby on Eden,Carlisle and out to the Solway Firth. Low lying land and roads are expected to start flooding first thing in the morning.
A flood alert has been issued for the Scottish Borders.
The Scottish Environment Protection Agency say that heavy rainfall throughout the day, combined with melting snow may result in localised flooding.
The areas most at risk are in the west of the region.
A flood alert has been issued for the Upper Derwent, from Seathwaite to Derwent Water.
The Environment Agency say further heavy rain is forecast throughout Friday, which will result in the rivers and lakes rising further.
Higher levels of water than yesterday are expected.
A flood alert has been issued at Port Carlisle, due to the high tide at 11.45am.
Low lying land and roads along the Gretna to Silloth coastline may be affected by flooding, before and after high tide.