Several causeways were flooded, particularly in the Uists, as water washed over the roadways in the hours after the 7am high tide.
But all causeways, including North Ford and Baleshare which were badly hit, had reopened by lunchtime.
However, police warned motorists of possible debris still on the roads.
Stornoway town centre was shut to traffic for a time in the morning, with North Beach Street particularly affected.
There was also flooding on Barra, including just past the airport terminal on the road to Eoligarry.
An electricity pole was also reported to have fallen on the road in the village of Floddabay, Harris.
Skye Bridge was closed to high vehicles, as were Kessock Bridge in Inverness and Dornoch Bridge.
Ferries hit by high winds
With winds of over 70 mph in areas, ferry services have also been severely affected with operator CalMac asking travellers to be patient and to check their sailings well in advance.
The Uig-Tarbert - Lochmaddy service was running with an approximate two hour delay.
Elsewhere on the Sound of Barra service the 9.25am and 11.10am sailings from Ardmhor and the 10.15am and 1pm sailings from Eriskay have been cancelled.
On the Stornoway to Ullapool route, the 7am and the 10.25am Ullapool sailings were also cancelled.
The Sound of Harris service - Berneray to Leverburgh - is also suspended
CalMac Ferries has apologised for disruption, while calling on travellers to be as flexible as possible when planning their journeys with bad weather set to continue.
A CalMac spokesman said: “We have been advised that there will be periods of severe weather hitting Scotland over the coming days and as a result our services may experience cancellations and/or disruptions.
“Due to the impact of this weather it is likely that our timetables and sailings will change at very short notice as we endeavour to maintain lifeline services.
“We fully appreciate that these disruptions will be inconvenient but the safety of passengers, crew and ships is our number one priority.”
Flood warnings across Scotland
In Dumfries and Galloway a man was seen swimming down the River Nith between Whitesands and Kingholm Quay while the river was in full spate. He was later traced by police and found to be safe and well.
Police Scotland warned people not to engage in activities likely to endanger their lives and the lives of the emergency services who may be called upon to rescue them.
The force said: “Those who engage in this type of activity need to appreciate that whilst they may feel confident in their ability, there are hidden dangers within the water such as trees and debris over which they have no control.”
Dumfries and Galloway Council said that properties were flooded at Isle of Whithorn, Portpatrick, Garlieston, Kirkcudbright, Annan, Carsethorn, Powfoot and Port William.
The harbour was also flooded in Garlieston and Kirkcudbright.
In Powfoot three families were evacuated to a farmhouse from Queensberry Bay Caravan Park while one person was evacuated from Creetown and a few families chose to leave their homes in Port William.
Headteachers in the region have been instructed to check whether they have any concerns that might affect schools reopening on Monday.