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Homes were hit as streets turned into rivers after more than 24 hours of torrential rainfall and thunderstorms.
And the rain is expected to continue to fall across the country throughout this week.
Properties in the Culloden, Balloch and Smithton areas, near Inverness, were affected by flood waters.
Police closed Murray Road and Murray Terrace in Smithton, and Barn Church Road, Culloden, and said the A96 Balloch junction was "badly flooded".
There were also flash floods in Perth and Balerno, Edinburgh, where there were lightning strikes during a storm.
The Met Office's Dave Clark said: "The winds are so light that it creates convergence zones, where the wind comes from several directions to one spot.
"This can create intense rainfall."
Northern Constabulary said other roads in the Highlands were affected by "significant surface water". A weather warning was in place, advising of further rain in the Moray Firth basin and Highland area.
Tayside Fire and Rescue Service said they had received more than 40 calls in just over two hours as torrential rain hit the Perth area on Saturday.
Calls were received from residents in the Feus Road, Crieff Road, Fairfield, Hillyland, Cherrybank, Letham, Bridgend and Gannochy areas.
At the height of the flooding on Saturday, firefighters rescued two elderly residents who had become trapped by flood water in the Bridgend area of Perth.
One local publican said: "It was the worst rain I have ever seen. The streets ran like rivers - the drains couldn't cope."
Scottish Environment Protection Agency flood warnings were in place across most of eastern Scotland.
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