Scotland's road and rail network hit by flooding
Train operators have been working to fully restore services after heavy rain caused disruption in Glasgow and Edinburgh.
Parts of Scotland saw rain in the last two days which was above average for this time of year, resulting in almost 30 flood warnings and 14 flood alerts.
It has also been reported that Glasgow saw one of the wettest 24-hour periods since records began.
More rain has been forecast over the next few days.
Showers may ease off, but the Met Office said on-going disruption was likely, because of flooding from standing water and from swollen rivers and streams.
Problems overnight and into Thursday morning forced ScotRail to reduce service between Glasgow Queen Street and Edinburgh Waverley.
And there was disruption between Edinburgh and North Berwick and Glasgow Queen Street and Dunblane.
ScotRail managing director Steve Montgomery urged travellers to check the operator's website for the latest information, adding: "We ran 86% of services across Scotland this morning, despite extraordinary rainfall levels in some areas."
Amid forecasts of further rain, Transport Minister Keith Brown asked the public to check before they travelled.
"Heavy rain overnight and today has caused some disruption to rail services this morning with some delays and cancellations but Network Rail and ScotRail are working to reduce the disruption and expect the services to improve throughout the day," he said.
Elsewhere, in Rosyth, water was pumped from homes and a school at Park Road.
There were also reports of small problems in Wellbank near Dundee, and at Ceres and Kilmany near Cupar.
Perth and Kinross Council announced that the Perth Highland Games, due to take place on Sunday, had been cancelled. The authority said this was because of the current bad weather conditions and the forecast of further rain.
Precautionary measures were taken in the Meadows area of Huntly in Aberdeenshire for a second time in a week.
At about 01:00, residents in the neighbourhood were alerted by police that the River Deveron could burst its banks.
Grampian Housing deployed flood defence guards to doors and windows of about 50 homes.
BBC Scotland weather forecaster Stav Danaos, said: "It has been one of the wettest 24 hours in the Glasgow area since records began.
"The rain will begin to ease down this afternoon and become lighter with drier conditions following."
A spokesman for the Scottish Environment Protection Agency, said: "We expect to see a gradual rise in river levels. But as rain is persistent rather than thundery downpours, we do not expect to see any sudden increases.
"Accumulation of surface water and standing water is also anticipated."
Dumfries and Galloway Police said drivers would need to take extra care on the roads, in anticipation of heavy rain.
Tayside Police said river levels were very high in the force area, but there were no reports of significant flooding, although officers urged motorists to take care.
Fife Fire and Rescue Service said they had six call-outs about flooding since 23:00 on Wednesday.