Sepa said areas of the southwest and Argyll, including the Solway Firth and Firth of Clyde, would experience volatile conditions, with large waves and strong winds.
They said flooding of low-lying land was likely.
In Shetland, Sepa warned “storm surges” could lead to waves overlapping in coastal areas, with the possibility of debris being displaced onto roads.
They said damage to properties near he shoreline was possible.
The Scottish Fire and Rescue Service was called to pump a “huge volume of water” away from a care home in Saltcoats on Sunday everning.
Dozens of alerts, external were issued across the country during the weekend and flooding also closed a number of roads, including the A78 Inverkip Road in Greenock; the A77 at Lendalfoot in Ayrshire; and several in Dumfries and Galloway.
Two women were injured by a falling tree near Aberfeldy Footbridge, also known as the “bouncy bridge”, in Perth and Kinross, and taken to hospital for treatment.
In South Ayrshire, police evacuated dangerous buildings in Ayr and helped 15 people stuck at a flooded caravan park in Ballantrae.