Roads have been closed and trains and ferries are either being delayed or cancelled.
Tayside Fire and Rescue Service said it was dealing with a major flooding incident in Comrie village, near Crieff in Perthshire, after the Water of Ruchill burst its banks. Ten fire engines are at the scene and a large part of the village is flooded.
Properties have been flooded in Dunblane, Aberfoyle and Callander, a spokesman for Central Scotland Fire and Rescue Service said. The main street in Aberfoyle is closed in both directions, police said.
A landslip has closed the A83 in both directions at the Rest and Be Thankful in Argyll. A diversion route has been set up.
Flooding has also closed the A814 in both directions at Rhu, between Helensburgh and Faslane. Motorists heading to Faslane or Coulport should use the A817 Haul Road or other alternative route.
High winds have seen the Forth Road Bridge closed to double-decker buses and it currently has speed restrictions.
Earlier traffic was queuing on the M8 because of flooding at junction 19 (Anderston Cross).
Trains between Glasgow and East Kilbride are disrupted by flooding at Thornliebank station and trains through Bishopton are also affected, ScotRail said.
Ferry operator CalMac listed 13 disruptions on its website, including to ferries between Wemyss Bay and Rothesay, Mallaig and Armadale, and Ardrossan and Brodick.
Increased risk of localised flooding has led to the Met Office issuing "be aware" warnings for central Scotland, Tayside and Fife, Highlands and islands, the south-west of Scotland, the Lothians and Borders and Strathclyde.
Five flood warnings have been given by the Scottish Environment Protection Agency within the Tayside area and for Pollok Country Park in Glasgow, as well as seven other flooding alerts for Argyll and Bute, Ayrshire and Arran, Central Scotland, Dumfries and Galloway and Skye and Lochaber.
Helen Rossington, forecaster at Meteogroup, said around two inches (5cm) of rain has fallen since 6pm yesterday, according to a rain gauge in Bishopton.
"It is no surprise there had been flooding overnight and this morning. Throughout the rest of the day the rain will become lighter and will move away to the east," she said.
"Wind speeds have been between 40mph-45mph, with southerly gusts of up to 50mph in more exposed areas."