It was feared the Forth estuary area would be affected by high tides coupled with a large storm surge.
People were advised to avoid coastal promenades this afternoon.
Riverside Drive in Aberdeen was closed for an hour after the River Dee burst its banks and there was some flooding in Garmouth, Moray, from the River Spey, police said.
No major incidents have so far been reported but 21 flood warnings and a further 16 alerts remain in place this evening.
The Scottish Environment Protection Agency (Sepa) said the any flooding today was likely to be less severe than experienced in some areas during storms at the beginning of December.
"River and loch levels remain high, but the picture is generally improving with some respite until further rain on Sunday afternoon," the agency said in a statement earlier today.
"There is no immediate prospect of an end to the unsettled weather, which means the situation will be kept under close observation and further alerts and warnings will be issued as necessary."
Motherwell's home match with Inverness Caley was called off this morning because the pitch at Fir Park was waterlogged. Some seven inches of rain have fallen in the area in the last 19 days.
Yesterday homes were flooded and people evacuated as a tidal surge combined with rain and 60mph winds battered the country.
In Scotland the west coast bore the brunt, with waves crashing over esplanades and roads engulfed in water in Ardrossan, North Ayrshire, and Dumbarton, West Dunbartonshire.
Dumfries and Galloway was also badly affected by flooding.
In Powfoot three families were evacuated to a farmhouse from Queensberry Bay Caravan Park while one person was evacuated from Creetown and some families had to leave their homes in Port William.
Properties were flooded at Isle of Whithorn, Portpatrick, Garlieston, Kirkcudbright, Annan and Carsethorn.
The Met Office has issued a yellow rain warning for Sunday afternoon and evening in south west Scotland, moving into the central belt.
Environment Minister Paul Wheelhouse urged members of the public to remain vigilant.
He said: "Scotland's agencies are continuing to work hard to provide a coordinated response to these difficult conditions and I'd like to pay tribute to the dedicated efforts of everyone involved.
"After the excellent efforts of the responders on the west coast, now services across the east are ready to react swiftly to minimise the impact of flooding."
Transport Minister Keith Brown said: "The advice, as always, is to prepare in advance for any travel. People should drive to the conditions, adhere to police advice and allow extra time for any journeys they are planning to make.
"I would urge anyone making a journey to check relevant websites such as Traffic Scotland for up to date travel information.
"We are in regular contact with the Met Office, Police Scotland, operating companies and Network Rail as well as the ferry operators and will continue to monitor weather events to ensure the maximum response to any incidents that arise."
In England and Wales, the storms caused more damage, with miles of coastline battered and roads and fields across the country left under water.
Prime Minister David Cameron praised the "great work" of the emergency services and Environment Agency in responding to the latest floods and defended the Government's flooding policy in protecting 200,000 homes.
The Environment Agency warned that the south and west coast of England and the Severn estuary still remain at risk of coastal flooding throughout the weekend and next week.
Communities along the north east coast, including Whitby and South Shields, could see flooding, while parts of the south coast, such as Portsmouth and Newhaven, may get more coastal flooding over the next two days.
Meanwhile, searches resumed in south Devon for missing 18-year-old university student Harry Martin who was last seen leaving his home to take photographs of the weather - with more than 100 people volunteering to look for him.
Two people have already died in the storms. A 27-year-old man from Surrey was found on Porthleven Sands beach in Cornwall after he was swept out to sea on New Year's Eve night, and a woman died after being rescued from the sea in Croyde Bay, north Devon.
Officials around the country have pleaded with people to keep away as dozens put their life at risk by going to coastal areas to watch as the storm brought waves up to 40ft high crashing on to land.
A man and child were almost swept away by a huge wave at Mullion Cove in Cornwall as they peered over the sea wall to watch the raging sea, and elsewhere in Cornwall vehicles driving on a coastal road were swamped and almost washed away by a tidal surge.
Elsewhere in Cornwall, Sergeant Regie Butler pulled a man who had been drinking from the sea at Towan Beach, Newquay after he had ignored police warnings about the fierce storms.
And in Aberystwyth, Dyfed a man was rescued by lifeboat after he defied police warnings and became trapped when photographing waves from a harbour jetty.
An RNLI spokesman said: "We repeat our warning to the public to stay safe and to keep away from the shore line and dangerous waves.
"This incident highlights the dangers posed not only to the man taking photos, but also the danger that our volunteer crew members and other emergency services have been placed in rescuing this man."
The ferocious weather has left widespread damage.
In Aberystwyth debris was strewn across the promenade, rail lines in north Wales were left buckled by the power of the sea and a road collapsed in Amroth, Pembrokeshire.
The storms in were said to be the worst to batter the Welsh coast in 15 years.
Aberystwyth University has deferred the start of the examination period by one week and was advising students not to travel to the coastal town until the middle of next week.
Geography student Millie Farmer said the town's promenade was a "complete mess" and estimated hundreds of thousands of pounds worth of damage had been done.
"They're starting to clear up. It's a complete mess," said the 19-year-old.
"You can't see the road. The promenade slabs have been scattered everywhere. It's an extension of the beach. It's a real shame."
Emergency services rescued four people from a flooded farm in Llanbedr near Barmouth, north west Wales, the River Severn burst its banks in Gloucestershire for the second day running and a pregnant woman was rescued after 30 properties were flooded in Cardigan, mid-Wales. Part of the sea wall behind the Landmark Theatre in Ilfracombe collapsed because of the storms.
People across the UK, from Devon to Cumbria and Sussex, protected their homes with sand bags and flood gates as the waters rose around them.
Currently in England and Wales there are no severe flood warnings in place but there are 99 flood warnings and 256 flood alerts in force.
As well as coastal areas, further heavy rain inland has left ground saturated - increasing the risk of river and surface water flooding.
In particular, there is an increased risk of flooding to Weybridge and Guildford in Surrey, while communities along the Thames, including Oxford and Osney, could also be at risk.
Also in danger are communities along the River Severn in Gloucestershire and on the Somerset Levels.
Rivers are also likely to rise in response to the rainfall in Dorset, Hampshire and Wiltshire. Further wet and windy conditions forecast over the weekend could exacerbate problems in already saturated areas.
The EA said that the most recent estimates suggest that around 90 properties have flooded since Friday, bringing the total number of properties flooded to around 220.
The coastal surge in recent days has tested over 3,000km of flood defences in England and over 205,000 properties have been protected.
The Thames barrier was again closed in the early hours and will continue to close to protect land near the river.
Jonathan Day, flood risk manager at the EA, said: "The risk of flooding to the coast will continue over the next few days, especially on the south and west coast and along the Severn estuary.
"In addition, wet conditions have left the ground saturated in many areas, increasing the risk of river and surface water flooding.
"We have protected over 200,000 properties across the country over the past 48 hours, and the Environment Agency will continue to work around the clock to protect communities."
Trains have also suffered disruption with services in west Wales and from Newport and Bristol to the south coast affected by the weather. There were also delays at the Port of Dover because of force five winds.