Forecasters said persistent rain was expected in central and southern areas today and into tomorrow.
Dumfries and Galloway, the Scottish Borders, and parts of Strathclyde and Tayside could be badly affected, with potential for flooding.
A yellow “be aware” warning for wind was also issued for much of the country for today.
The Met Office said: “A waving cold front is expected to become slow-moving over western Britain during Tuesday night and for much of Wednesday, associated with a strong, moist south-westerly airflow.
“Rainfall accumulations through this period are expected to be widely 20-40mm (0.8-1.6in), with 80mm (3.2in) over some higher ground within the area, and the potential for some exposed locations in south-west Scotland to receive 100-150mm (4-5.9in).”
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Last night, the Scottish Environment Protection Agency issued a flood warning for the Glen Lyon area meaning that flooding was expected and that immediate action was required.
Transport minister Derek Mackay urged motorists to plan ahead for their journey.
He said: “Surface water and spray could make driving conditions difficult and there may be some localised flooding. We will have patrols on the main routes to do all they can to keep the roads running and our teams out on the network to clear drainage systems in advance of the heavy rain.
“Drivers should travel with extra care and drive to the conditions. We strongly advise all road users plan their journeys in advance by checking the Traffic Scotland website and Twitter feed for the latest information before setting off on your journey and factor in extra time as travel may take longer than usual.
“Listen to police advice and take conditions into account when planning your journey.”