The Met Office issued a warning about another band of heavy rain that was expected to hit the morning rush hour.
Motorists in Glasgow were being warned about surface water on the city's roads, with up to 25mm of rain predicted to fall through the day.
The heavy rain is expected to continue up until the weekend, with 40mm of rain predicted on Thursday – well over a quarter of the average monthly rainfall for November.
A number of roads in the Central Belt were closed yesterday as a result of Sunday night's heavy rain.
Glasgow was lashed with around a quarter of the average monthly rainfall for November on Sunday night through to yesterday morning.
Between 6pm and 6am, 34mm of rain fell – the monthly average for November is 132mm, althought temperatures remained on the mild side.
The bad weather caused road closures and train disruption.
On the M8, between junctions 11 and 12 at Queenslie, a three-car collision saw two lanes closed eastbound.
ScotRail services between Glasgow and Gourock were cancelled and trains from Largs into the city were starting at West Kilbride, all due to flooding.
Flooding on the line at Bishopton in Renfrewshire was also causing delays and services to Thornliebank were also affected for part of the day.
A spokesman for Network Rail said: "One of the problems we have had is that the rainfall is quite localised.
"A lot of water has been falling in Glasgow. It is not getting a chance to drain away.
"We are continuing to monitor areas where we might expect to get flooding.
"We have mobile pumping units, which we can use to pump the water out, and pumps at fixed points."
The Met Office had yellow "be aware" warnings in place for Strathclyde, Central, Tayside & Fife, Grampian, Highlands & Eilean Siar, SW Scotland and Lothian and Borders.
Strathclyde Police was forced to evacuate police dogs and vehicles from the force's training centre in Pollok Park after it became severely waterlogged.
Playing fields in Thornliebank in East Renfrewshire were completely submerged.
CalMac ferries between Largs and Cumbrae were suspended yesterday due to high winds and Argyll Ferries' services between Gourock and Dunoon were also called off.
Renfrewshire Council dealt with nearly 50 flooding incidents in 24 hours.
Over the course of the day Lochlip Road, in Lochwinnoch, Candren Road, between Paisley and Linwood, Murray Street, in Paisley, and Kibbleston Road, in Kilbarchan were all closed.
Councillor Jim Harte, Convener of Renfrewshire Council's Environment and Infrastructure Policy Board, said: "We will continue to monitor the weather and we have employees ready to deal with the situation as it develops."
There were road closures in Kilmacolm, Dumbarton and Old Kilpatrick due to floods.
Elsewhere there were reports of serious flooding in central Scotland and the main street in Aberfoyle had to be closed due to severe flooding.
The Rest and Be Thankful section of the A83 in Argyll was shut both ways after a landslip, the fifth time falling debris has closed the road in five years.
There will be some respite from the heavy rain tomorrow, however Thursday will see between 30 and 40mm of rainfall.
Friday will be slightly more settled but the wet spell is expected to continue through the weekend.