Kirkwall lifeboat crews were called to assist officers and Coastguard teams at the pier, where divers were seen working throughout the morning.
An eyewitness told The Press and Journal: “Divers appear to be working in the water, and the RNLI are there, as well as a police car, van and ambulance.”
Harbour closed for hours
The linkspan was also closed for several hours with ferry services cancelled because of the incident.
Police have now confirmed there appears to be no suspicious circumstances surrounding the man’s death.
A spokesperson said: “Around 5.40am on Wednesday, May 8, the body of a 50-year-old man was discovered in the water at Kirkwall Harbour, Orkney.
“His next of kin are aware.
“There are no suspicious circumstances and a report will be sent to the procurator fiscal.”