The Scottish Environment Protection Agency (Sepa) said it had put an amber risk of flooding in place for the northern and Western Isles and Caithness and Sutherland.
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.
Highland Council said flood gates on the mile-long Caol and Lochyside flood protection scheme, near Fort William, had been closed following a warning from Sepa.
In Orkney, Police Scotland have closed the Churchill Barriers causeways which connect the mainland to the islands of South Ronaldsay, Burray, Lamb Holm and Glimps Holm.
The main road through the village of St Mary’s Holm has also been closed due to flooding caused by high winds and high tide.
Police Scotland said a high risk of disruption remained with poor weather conditions expected on Tuesday.
Police Scotland Assistant Chief Constable Mark Sutherland said that, although the amber weather warning was no longer in place, disruption was “likely well beyond that due to further poor weather, fallen trees and other damage caused by the storm”.
Social Justice and Housing Secretary Shirley-Anne Somerville told BBC Scotland News there were “challenges ahead” due to the prolonged nature of the conditions.
She urged councils to review their readiness, adding authorities were working to ensure that “everything that can be done is being done”.
Somerville also said that everyone can play a part by getting “households as resilient as we can, as well as looking after neighbours and friends”.
