Parts of the town were engulfed by up to four-and-a-half feet of water and weather forecasters have warned that more rain could be on its way on Monday.
Coastguards and lifeboat crews were called to evacuate 200 guests from a hotel and the residents of about 15 nearby homes.
Delays were continuing on many roads in the area and part of the east coast main line was washed away, disrupting rail services to Glasgow, Edinburgh and England.
A police spokesman said: "It is localised in the Inverness area. Ten miles down the road there's nothing. It's just a freak incident."
'Ferocity'
The Highlands and Islands Fire Brigade said it received about 180 calls for help, mostly from people whose homes were flooded.
Sandbags were distributed to the worst affected areas, but some homes are thought to have suffered extensive damage.
Local councillor David Munro said the floods had been a "disaster" for the city.
He said: "I've never seen anything like the ferocity of the rain. It has been like a fireman's hose on full pelt.
"I can remember floods before, but nothing like this - roads have been washed away, cars have been floating down on the current and communities are cut off."
Honeymoon
Among the 200 people evacuated from the Thistle Hotel were newlyweds Jackie and Andrew Torrie, from Alness, Easter Ross.
Mrs Torrie, 26, said: "The first I knew about the flooding was a member of staff banging on the door about 7am to tell us.
"I looked out and saw cars floating about in the car park - including ours - and thought my honeymoon was ruined.
"All our going away clothes were in cases in the car and we had were planning driving to Glasgow to catch out flight to Tenerife."
Andrew, 27, said firemen had waded out to the car and salvaged the cases, which had survived the worst of the damage.
"The Tenerife sun will soon dry us out, but at one point I thought I would be heading for honeymoon in my dress kilt outfit," he added.
Landslide
Most roads had been reopened by Monday morning, but there were still problems on some routes.
A police spokeswoman said that the A82 from Fort William to Inverness was closed at Abriachan due to a landslide, but diversions were in place.
A slip road off the A9 northbound at Raigmore Interchange was likely to be closed for a week, because of damage caused by the flood waters.
The B9039 Newton to Ardersier road - the main route to the city's airport - was also closed.
Rail services to the east and south of Inverness were expected to be out of action for at least the next couple of days.
Highland Council has also set up a 24-hour helpline, on 0800 838009.