A second severe flood warning has been issued for properties in part of Perth.
The warning covers the North Inch area of the city. A warning is already in place for the Dalfaber area of Aviemore.
The Scottish Environment Protection Agency (Sepa) says properties in basements and low-lying areas of North Inch are being flooded.
A Met Office Amber rain warning for some parts of the Highlands and north east of Scotland expired at 14:00.
Meanwhile, work has begun to clear the A83 after seven landslips blocked the vital road to Argyll and the Inner Hebrides on Saturday.
Hours of heavy and persistent rain on Friday and Saturday dumped water and about 2,000 tonnes of debris along the route.
Ten people had to be airlifted from their vehicles on the A83 at the height of the bad weather.
The area around the Rest and Be Thankful saw a month's worth of rainfall, about 160mm (6in) fall over 36 hours. Bear Scotland said the catch pits and fences it installed had ensured that only a small amount of debris reached the road itself.
Road closures are in place between Inveraray and Tarbet due to landslides both sides of Dunoon junction. The diversion via A819/A85/A82 at A85 Dalmally is open.
The Western Ferries route from Gourock to Dunoon is running.
The clear-up has begun on the A83 after it suffered seven landslips
Ian Stewart, Bear Scotland's north west representative, said: "This extreme weather has caused widespread disruption, with Argyll significantly affected.
"Our teams are beginning clear-up operations to return full access to residents of Argyll, but conditions are still difficult, and we need to ensure that those on site are safe. As such, it is unlikely the A83 will reopen today.
"We are also continuing to work as part of the Argyll and Bute Resilience Partnership to assess road closures and incidents in the area."
Sepa also has 53 flood warnings and 11 flood alerts in place.
Police said on Saturday there had been no reports of injuries but they were treating the persistent heavy rain in parts of the west of Scotland as a "major incident".
The Met Office said Tyndrum, west Perthshire, experienced the most rainfall on Saturday, with 112.6mm (4.4in) falling on the small village.
The River Spey burst its banks at the Old Bridge Inn at Aviemore
In Aberfoyle, a warning was issued by NHS Forth Valley after a lorry overturned, spilling kerosene/diesel into the watercourse. It said kerosene had also leaked into the general floodwater which poses a potential threat to public health.
Health protection experts urged people to be extra careful if floodwater had entered their homes as there could be "significant health risks" to certain groups such as pregnant women, children, the elderly and those living with heart and lung conditions.
There following trunk roads are closed:
- The A84 between Kilmahog and Strathyre
- A92 at Letham
- A83 between Tarbet and Inveraray
- A828 between Connel and Ballachulish
- A85 at Loch Awe
ScotRail said disruption was continuing on Sunday with the following routes completely closed:
- West Highland Line between Glasgow and Oban/Fort William
- All services between Edinburgh and Perth, Dundee, Aberdeen, and Inverness
- All services between Glasgow and Perth, Dundee, Aberdeen, and Inverness
- All services between Kyle of Lochalsh and Inverness
ScotRail is advising customers not to travel as no rail replacement travel is available. Some other routes remain affected by speed restrictions as a safety precaution, meaning services may be subject to delay or cancellation.
This flooded sports field is in Kingussie
David Simpson, ScotRail service delivery director, said: "The weather we have seen over the weekend has been extreme and in some parts of the country we are continuing to see dangerous levels of rainfall and flooding. We appreciate that weather-related disruption like this can be frustrating, but our first priority has to be the safety of the public and our colleagues.
"Our staff across the country, alongside colleagues at Network Rail, are working hard to get services back to normal as quickly and safely as possible, with the priority being getting things back to normal for Monday morning.
"Customers are advised that they should check their journey before travelling, and keep an eye on our website, app, or social media feeds for live updates."
The River Spey levels were very high in Aviemore
Roads in Aviemore were covered in water
Vincent Fitzsimons, Sepa's flood duty manager, said: "It's been a rough weekend across Scotland, with severe weather causing widespread travel disruption to road and rail networks and impacts in communities from Greenock to Aviemore.
"Our teams have been working around the clock with Scottish government and the Met Office in the lead into and across this major weather event. We have been issuing alerts and warnings to communities at risk and supporting first responders.
"Today the focus continues to turn to communities across the north, with a particular concern for severe flood impacts to communities along the Spey and Tay rivers. It's a day to stay alert, not stand down. The risk to life remains.
"We'll be issuing further updates across the day to communities across northern Scotland and our advice remains for people to keep up to date with information from sepa.org.uk and follow guidance from emergency services."
On Saturday no cross border trains ran and ScotRail cancelled dozens of services and also cut short its scheduled timetable.
Road maintenance agencies said that conditions in the Argyll area were "challenging" and it was too dangerous to assess the A83 landslips on Saturday.
The Craigie area of Perth was flooded after the Craigie burn burst its banks
The A83 has proven especially vulnerable to landslips and closures and in recent years calls have grown for a permanent solution to make the road more resilient to bad weather.
At almost 100 miles (161km) long, the road connects the Mull of Kintyre and southern Argyll to the shores of Loch Lomond. About 1.3 million vehicles use the route every year.
The closures can leave motorists facing long detours while the route is cleared.
Transport Scotland is planning to build a mile-long open-sided tunnel on the road, on the mountain pass known as the Rest and Be Thankful. The project is expected to cost up to £470m.
Posting on X, the social media site formerly known as Twitter, the former Argyll MSP Michael Russell said: "The amount and rate of rainfall here in Argyll & Bute in the last 24 hours has been astonishing.
"However, that aside it is concerning that slips are on this stretch which is not the area where most of the major problems have previously occurred."
Steps under water at the River Dee at Banchory
An Argyll and Bute Council spokeswoman said: "We are working with our partner agencies, including Police Scotland, the HSCP (Health and Social Care Partnership) and others, to respond to the impact of this weekend's weather in Argyll and Bute.
"We have well established partnership arrangements for supporting vulnerable people and have put them into action. Actions have included for example preparing a rest centre yesterday in Lochgilphead for people potentially stranded because of road closures, although this ultimately was not needed.
"There are road closures across the area because of landslips, flooding or other impacts, and advice remains to not travel in Argyll and Bute.
"We have road crews out across the area to continue work today to clear debris on the road network where possible and to assess the impact of weather conditions, and the recovery work needed.
"Many people in our communities also took action to help and we would like to thank everyone involved for their efforts."
An abandoned car under a flooded railway bridge in Dumbarton, West Dunbartonshire
In the south of the UK, sunshine and highs of about 25C (77F) were forecast by the Met Office for Sunday.
Tom Morgan, a Met Office meteorologist, said the contrasting weather was caused by warm weather travelling up from France meeting cold weather coming from the north with the temperature contrast leading to the heavy rain in Scotland.
The warm weather in southern parts was expected to last until Tuesday.
