The Scottish Environment Protection Agency (Sepa) has issued dozens of warnings, most of them in Tayside.
People in the Borders and Dumfries and Galloway have been asked to pay close attention to the weather forecast over Christmas Day into Boxing Day.
Warnings were also in place on Christmas Eve covering Strathglass and Callander.
Storm Eva is expected to bring further bad weather to areas which have already been badly affected.
A weather warning of heavy rain is in place for much of southern Scotland from 15:00 on Christmas Day through to 23:45 on Boxing Day.
Many roads across Dumfries and Galloway were affected by surface water or flooding on Christmas Eve and drivers were asked "slow down and take care".
The A76 Dumfries to Kilmarnock road near to Drumlanrig Castle was reported as "flooded but passable".
The B724 Annan to Dumfries "low road" was flooded with a road closure in place west of Cummertrees.
In Dumfries itself, the Whitesands car parks were closed due to flooding in the area.
High winds also affected the north of Scotland on Christmas Eve with gusty of 60mph to 70mph forecast and up to 80mph over the Western Isles.
Eleven out of 26 Caledonian MacBrayne routes were disrupted but the situation was improving.
Passengers were asked to check on the website, on Twitter @calmac_updates and also on the freephone number 0800 066 5400 for regular updates.

Datawind was among four finalists in a competition organised by UK Trade and Investment.
The firm hopes the Ubislate, which sells for Â£22 ($35), will make digital connectivity more affordable.
The three other finalists in the Smart UK Project were Blippar, P2i and QRpedia.
Seventy-nine UK-based companies entered the competition in December.
A key factor in selecting the finalists was that they demonstrated the potential to become global businesses.
The winner of the competition was announced at the Mobile World Congress in Barcelona.
As well as the prestige of winning, Datawind will get free design consultancy and free software.
Russell Buckley, one of the Smart UK Project judges, said: "We were very impressed by the quality of all the finalists.
"It was a tough decision but we are very pleased that Datawind has won.
"There is a global potential and the will to transform lives and society, all using the resources of a British company."
Suneet Singh Tuli, chief executive of Datawind, said the result was a "great validation of our vision".
Many parts of Scotland are at risk of flooding over Christmas after more heavy rain affected the country.
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The makers of a 7in (17.8cm) Android tablet have been named "UK's Most Innovative Mobile Company".