Parts of the west coast have been the worst hit, including towns such as Ardrossan, North Ayrshire, and Dumbarton, West Dunbartonshire, with waves crashing over esplanades and roads engulfed in water.
There are almost 40 flood warnings in place for Argyll and Bute, Ayrshire and Arran, Dumfries and Galloway, Skye and Lochaber, Tayside and west central Scotland.
Flood alerts have also been issued for locations including central Scotland, Dundee and Angus, the Scottish Borders and Orkney and Shetland.
The tidal surge was expected to peak at about lunchtime.
The Met Office has issued further warnings for poor conditions combined with significant tidal surges in the Firth of Clyde, Solway Firth, the Minch and the Ayrshire coast.
The conditions have caused travel disruption, with the A78 closed in both directions between Stevenston and Kilwinning, and between Skelmorlie and Largs.
In Dumfries and Galloway, the Kelton to Glencaple road was blocked while Annan Harbour area was also flooded.
Police Scotland reported that flooding had occurred on the A747 between Glenluce and Port William, and at Carsethorn, Powfoot and Newbie.
P&O Ferries has suspended its ferries from Cairnryan in Dumfries and Galloway to Larne in Northern Ireland.
The Forth Road Bridge has been closed to high-sided vehicles while Traffic Scotland has urged drivers to be cautious, with surface water affecting conditions on some roads.
Scotrail warned that train services between Glasgow Central and Ardrossan Harbour, Glasgow Central and Largs, and Edinburgh and Helensburgh Central via Airdrie may be delayed or disrupted. Replacement bus services are in place.
Environment minister Paul Wheelhouse visited the Police Scotland Communications Centre in Govan to see activity in response to the severe weather while another meeting of the Scottish Government's Resilience Room (SGoRR) was chaired by the First Minister.
Mr Wheelhouse said: "Preparedness for flooding events such as those experienced by Scottish communities in the past week is key.
"I have seen from Police Scotland cameras that emergency responders are working extremely hard in locations around the country to provide a co-ordinated response to these difficult conditions.
Mr Wheelhouse also said there had been high tide levels in Fort William and Oban this morning but sea defences had not been breached.
"We have, however, had some flooding in Stornoway and that's something that wasn't necessarily predicted," he said.
"Ferry services in many cases have been delayed or cancelled and we have some rail disruption on the Ardrossan line, where there's a known trouble spot with salt spray from the sea causing electrical problems on the line.
"We also have some road closures because of the risk of coastal flooding."
"I'd like to pay tribute to the dedicated efforts of all the agencies involved in tackling flooding."
Transport minister Keith Brown said: "Today's conditions are leading to some isolated incidents on the network and Transport Scotland is monitoring the situation from our Traffic Control Centre.
"The flood gates on the A78 at Skelmorlie were closed by Police Scotland earlier this morning and the route will not reopen until this afternoon after the high tide.
"The trunk road operating companies are patrolling the vulnerable locations on the coast and are working with local authority counterparts to mitigate the impacts and provide alternative diversion routes where appropriate.
"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.
"We advise to check relevant websites such as Traffic Scotland for up-to-date travel information."
The minister added: "We know already there's another low pressure system hitting us on Sunday but we don't know yet how severe it will be.
"There's no particular signal that it's going to be a particularly bad one but because of the degree of saturation of the ground that we have at the moment, any rainfall of significance can trigger local flooding."