Emergency services were called to the River Findhorn in Moray shortly after 12.30pm on Wednesday after the man got into difficulties on the water.
Police Scotland confirmed that the body of the man, who was in his 50s, was recovered from the river at around 9am on Thursday.
The kayaker has not yet been named by police. His family have been told.
The man got into difficulties while navigating near an area known as Elephant Rock, police said.
His body was recovered with the help of a coastguard river team. A report will now be sent to the procurator fiscal, officers said.
News of the man’s death emerged as communities affected by flooding north of the border assessed the damage caused by the storm, which left people stranded, in temporary accommodation and without electricity.
Large parts of the country were affected by Wednesday’s heavy rain and gale-force winds, which prompted the most severe “danger to life” flood warnings to be issued for a time.
Dozens of homes were evacuated as flood waters rose, forcing residents to spend the night in temporary accommodation.
Emergency services who carried out a “major multi-agency response” to severe flooding in Peebles in the Scottish Borders said they rescued six people who were trapped in their homes and cars and 25 people from a care home.
First Minister Nicola Sturgeon is visiting Newton Stewart in Dumfries and Galloway, one of the communities worst affected by the storm, to see for herself some of the damage caused.
Dumfries and Galloway Council said the major emergency in its area has now passed, with the exception of a few “legacy issues” including flooding at Carlingwark, Castle Douglas. River levels are dropping on most of the rivers across the region, the local authority said.
As the clean-up operations continue across the country, a number of flood warnings and flood alerts remain in place throughout Scotland – but many others have been lifted.
At the storm’s height, the Scottish Environment Protection Agency (Sepa) had issued a “severe flooding – danger to life” warning for Whitesands in Dumfries and Galloway and for the River Tweed in Peebles.
Aberdeenshire, Ayrshire, Dumfries and Galloway and the Borders bore the brunt of the severe weather, which caused disruption to road, rail and ferry services.
Twelve people, including two children, were rescued from a bus after it was stranded in flood water in Dailly, South Ayrshire, on Wednesday.
The Scottish Fire and Rescue Service (SFRS) said it had been involved in a “major multi-agency response” after the River Tweed burst its banks, flooding large areas of Peebles.
In Aberdeen on Wednesday, coastguard rescue teams were called to help evacuate a care home which was flooded.
Residents were also removed from the Riverside Drive area in the city and moved to Norwood Hall, which was opened as a rest centre.
In Aberdeenshire, homes in Anderson Road, Deebank Road and Albert Road in Ballater were evacuated and a rest centre was set up at the Victoria Barracks and nearby Aboyne Academy.
At the other end of the country in Newton Stewart, homes were also evacuated and a rest centre set up at Douglas Ewart High School.
The rain and gales left thousands of homes without power, with faults caused by wind damage and trees or other debris on the lines.
Scottish Hydro Electric Power Distribution (Shepd) said more than 100 of its engineers and technical staff are working in Ballater to restore power supplies.
Engineers reconnected supplies to properties overnight, where it was safe to do so, but the severe flooding that hit the village washed away some of the electricity poles.
By Thursday lunchtime, 200 properties were still off supply in Ballater, while another 250 were without power in the surrounding areas.
Hundreds of customers were also still off supply in areas such as Archiestown, near Aberlour in Moray, and Meikleour in Perthshire.
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