The A835 Ullapool was closed for several hours because of a landslide at Garve.
Police Scotland warned drivers to expect delays as the weather affected a number of roads across the country.
Emergency teams are also dealing with landslips on the A83 Rest and Be Thankful in Argyll and Bute and the A85 in Stirlingshire at Crianlarich.
The Old Military Road A83 diversion is now being used.
The road between Ardnarff and Strathcarron in the Highlands, on the A890 Stromeferry bypass, is likely to be closed for at least 12 hours after a large landslide.
A railway line next to the road has not been affected.
The Met Office issued an amber warning of rain for the Highlands, as well as yellow warnings covering parts of Perthshire, Fife, Strathclyde and the south west.
Drivers were advised to use the A87 as an alternative route between Kyle and Inverness.
The Stromeferry bypass in Wester Ross has been badly affected by landslides in the past.
One landslip closed the route from 22 December 2011 to 23 April 2012 and cost Highland Council Â£2.8m to deal with.
The bypass plays a part in taking traffic around Loch Carron.
Highland Council said the bypass was closed at 07:30.
A spokeswoman added: "Rain has stopped falling and ground conditions appear to be easing.
"Our initial assessment shows the landslip to be relatively small so we hope to have the road cleared and reopened later today. Police and engineers are on site at present.
"Trains are currently unaffected."
In Edinburgh, Balcarres Street has flooded. People living in neighbouring flats have put up their flood gates to stop the water from entering their homes.
Meanwhile, the A82 was closed for a short time earlier on Tuesday between Tarbet and Crianlarich. The section of road has been reopened under temporary traffic lights.
The A82 south of Fort William partially reopened on Monday after two landslides blocked the road on Sunday.
The Scottish Environment Protection Agency issued flood warnings for large parts of Perthshire and Tayside, Skye, Lochaber, Speyside and Easter Ross.
Flood alerts were also in place for Argyll and Bute, Wester Ross and Caithness.
In Aberdeen, a vehicle was stuck in floodwater under a footbridge near Stoneywood Road.
Firefighters have been pumping flood water from a filling station at Inverness' Inshes Retail Park, while travel on some roads in and around the city have also been affected by surface water.
Police warned of "heavy flooding" on both carriageways of the A90 in Dundee, and officers urged caution on the roads in the west, Highlands and north east.
Rail services between Gourock, Wemyss Bay and Port Glasgow have been affected by flooding.
In southern Scotland, a landslip between New Cumnock and Kirkconnel means trains between between Glasgow and Carlisle will terminate and start from Kilmarnock.
Alternative transport is being arranged for Kilmarnock, Dumfries and Carlisle.
The bad weather is expected to ease in many areas midway through Tuesday morning.
However, the Met Office said that since Saturday the worst-affected parts of the country had seen three-day rainfall totals in excess of 150mm (5.9ins).
And BBC Scotland weather presenter Chris Blanchett said 265mm of rain (10.4ins) had fallen in some parts of the Highlands since Friday.
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Landslides have closed several roads across Scotland as further heavy rains batter the country.