Police Scotland warned commuters in Aberdeen that both Market Street and Virginia Street in the city were closed due to flooding.
Areas including Stonehaven and Forres in the North East, and Kincardine and Falkirk in the Central Belt have also been impacted.
A photograph taken by a local resident in Kincardine shows the High Street completely submerged in water.
Meanwhile rail services between Perth and Stirling were disrupted by a landslip at Gleneagles.
ScotRail later confirmed that the line had re-opened.
It comes amid a yellow warning for rain covering much of the country until Thursday morning, which could see up to 120mm of rainfall in some areas.
A second, smaller amber warning for thunderstorms in is place across northern Scotland.
The Scottish Environment Protection Agency (Sepa) has also issued 15 separate flood alerts.
Yesterday, the Scottish Government’s emergency committee convened to respond to the alert and ensure preparations are in place.
Deputy First Minister John Swinney warned Scots against flooding, saying: “The decision by the Met Office to issue the amber warning for thunderstorms signals a potentially damaging and dangerous risk of flooding in some areas.
“Flooding could happen quickly, even in areas not usually prone to flooding.
“Some communities might become cut off if roads flood, and power cuts might occur.
“Please take extra care if you are out and about, do not attempt to walk or drive through flood water, avoid camping near watercourses and ensure water conditions are safe if spending time in the water.
“The Scottish Government is in close contact with local authorities and the emergency services to ensure people in the affected areas receive the latest information, advice and support where needed.”
Douglas Cairns, Traffic Scotland’s operations support manager, warned drivers of what could be hazardous conditions due to heavy rain.
“It’s important people plan their journeys before they set off and make sure their routes are available,” he added.
“The Traffic Scotland Twitter page is regularly updated and the mobile website, my.trafficscotland.org, lets people get the latest information on the move.
“If you are planning to travel by train, ferry or plane, please check with operators to see if the conditions are having any impact on your services.”