Thirteen flood warnings are in place for Tayside as the area continues to feel the effects of Storm Diana.
One area at risk is Coupar Angus, which is under strain from the River Isla.
A Sepa statement said: “Levels on the River Isla in this area responded to the persistent rainfall during Wednesday. River levels are expected high overnight into Thursday.
“There is a risk of overtopping of the agricultural embankments and flooding to low lying agricultural land.”
The area south-east of Blairgowrie is also at risk of flooding.
Sepa said in a statement: “A flood warning has been issued for Blairgowrie to the River Isla.
“River Ericht levels have responded to the persistent rainfall during Wednesday. River levels are expected to remain high overnight into Thursday.
“Low lying agricultural areas adjacent to the River Ericht is at risk of flooding.”
Here is a full list of areas subject to a flood warning:
The River Isla at Coupar Angus
Pitlochry to Ballinluig
Logierait to Jubilee Bridge
Kemphill to Bridge of Isla
Innerpeffray to Bridge of Earn
Crieff to Innerpeffray
Carse of Lennoch to Lochlane
Bridge of Ruthven to Leitfie
Blairgowrie to the River Isla
Ballinluig to Logierait
A yellow Met Office weather warning for rain remains in place until 2pm across large swathes of Perthshire and Fife.
However, Dundee is no longer subject to a yellow warning for wind. The Tay Road Bridge was closed to double-decker buses briefly overnight.
Elsewhere in the UK, weather warnings for gusts of up to 80mph and persistent rain have been issued for parts.
The Met Office has warned up to 35mm of rain could fall in parts of Scotland in six hours, while a vast swathe of the UK could be hit by “widespread strong winds”.
The country was hit by strong gusts on Wednesday – with Capel Curig in Snowdonia, Wales, recording gusts of 90mph, while Keswick, Cumbria, saw 47.4mm of rain.
The yellow warning for wind covers all parts of England except the south-east of England and East Anglia until 2pm.
The Met Office said: “Inland gusts of 50 mph are likely with gusts of around 65 mph in exposed locations around Wales and western England.
“There remains a very small chance that this system will intensify as it moves northeastwards bringing even stronger winds to southwest England, Wales and on into northern England and southeast Scotland.
“If this occurs, gusts of 70-80 mph could be seen, mainly in exposed locations.”
Meanwhile, a warning for rain covers central, Tayside and Fife, Grampian, the Lothian Borders and Strathclyde in Scotland.
Forecasters said: “Rain will become persistent and heavy again on Thursday morning and into the early afternoon, before clearing.
“Accumulations of 15-25mm are likely to fall in around 6 hours, with up to 35mm on higher ground.”