Only Arbroath has had their flood alert cancelled as Fife, in particular, continues to suffer from significant flooding.
Eight flood alerts have been issued by Sepa (Scottish Environmental Protection Agency) covering regions including Edinburgh and the Lothians, Scottish Borders, Tayside, Aberdeenshire and West Central Scotland.
Persistent rain and melting snow have caused flooding across the country.
ScotRail train services between Cowdenbeath and Glenrothes in Fife have been cancelled.
Train services between Edinburgh and Glenrothes With Thornton via Dunfermline have also been terminated and are being started back from Cowdenbeath.
Safety concerns have also forced a shutdown of the Edinburgh-North Berwick rail line due to overhanging snow falling onto the track in a cutting.
Trains running are instead stopping and departing from Drem. ScotRail said North Berwick would not be served today.
ScotRail said staff had been on site throughout the night, but a daylight inspection of one bridge in Fife needed must be carried out before train services could be restored along the route.
“Services between Edinburgh and Glenrothes via Kirkcaldy will run on a reduced timetable departing Edinburgh at approximately 10 minutes past the hour and departing Glenrothes at approximately 20 minutes past the hour,” a ScotRail statement said.
“Additional services during the morning and evening peaks will also run. Please check your journey before you travel.”
Passengers at Lochgelly and Cardenden were told to use bus services instead of the train.
Park Road Primary and nursery in Rosyth have been closed due to flooding, with Fife Council warning some homes nearby may also be at risk.
Police have also warned of severe flooding on the A92 between Dundee and Montrose.
A yellow - “be aware” - severe weather warning for snow and ice had been extended to 11pm yesterday covering much of Scotland north of the Central Belt away from the west coast.
Disruption from the 100m-long submerged section of the Edinburgh-North Berwick line is expected to continue until tonight.
A spokesman for the ScotRail Alliance with Network Rail said: “We’ve got eight pumps on site working to clear the standing water but we’re seeing significant amounts of snow melt in the area and water is building back up almost as fast as it can be removed.” Drivers were hit by heavy snowfall on roads south of Glasgow, including the M77 and A726 East Kilbride expressway. Congestion was also reported across the Central Belt with the M8, M80 and M77 motorways affected by sleet and snow during the morning rush hour.
The Met Office said: “A spell of persistent rain, with snow mainly affecting high ground, will continue to affect much of northern and eastern Scotland this afternoon and into the evening. “5-10cm of snow is likely to accumulate over higher routes, above 200m, with 10-15cm possible on the highest routes above 400m. Hilarious Kids’ Test Answers That Are Too Brilliant To Be Wrong Read More Give It Love “Below 200m, mostly rain or sleet is expected and 20-30mm of rain is possible along eastern coastal regions. “Delays to travel and public transport could occur from snow on higher ground. “Spray and flooding on low level roads will probably make journey times longer.”