The operation to clear up and assess damage caused by the storms and torrential rain of earlier this week got under way but the rail lines from Inverness to both Aberdeen and Perth remained out of action.
The Met Office said that some locations had twice the expected monthly rainfall in just two days. This led to significant flooding across both rail routes, which damaged parts of the track and signalling equipment and left bridges in need of structural inspections. Flood waters three feet deep at Kingussie washed away a section of the track bed.
Several other locations on the Highland main line to Perth, Glasgow and Edinburgh were left buried under mud and debris washed onto the railway by the severe weather. On the Inverness-Aberdeen line, the track remained underwater at several locations between Elgin and Keith, while the Lossiemouth viaduct was to be examined by specialist divers to ensure the structure had not been damaged. Today is the earliest that either line will open.
There was also disruption on the line from Inverness to Kyle of Lochalsh.
Alex Sharkey, Network Rail area director for the East of Scotland, said: "The sheer volume of water deposited on the tracks over such a short period of time has caused extensive damage in some locations.
"Our engineers are working around the clock to carry out all the repairs necessary for the safe reopening of the lines and we will restore a full service for train operators and quickly as possible."
Jacqueline Dey, operations and safety director, said customers using the sleeper service were being taken from Inverness to Glasgow by bus last night, offered refreshments at the Grand Central Hotel and would continue on their onwards journey to London on an early morning train.
The Scottish Government has said it will consider emergency funding for local authorities to help deal with the costs of flood damage after representations from Moray Council.
A spokeswoman for the Met Office said that in the 48 hours from 1am on Sunday to 1am yesterday, Lossiemouth had 121mm of rain. The average for the town in August was 61.9mm, while average for the whole of Scotland for the month was 116.7mm.
Meanwhile, a large area of rock fall has left a popular footpath in the Cairngorms in an unstable and dangerous state. Slabs from the cliffs above the Goat Track path in Coire an t-Sneachda, one of famous Northern Corries in the Cairngorms that help form the classic view from Loch Morlich, had fallen across the track and surrounding area.
Walkers and climbers were advised to keep away from whole Goat Track area.