The diver, understood to be male, went missing on Sunday afternoon. Police Scotland have also been supporting the efforts as searches continue.
A helicopter has been deployed, as well as lifeboat teams from the area, to help with the search.
A spokesperson from the Maritime & Coastguard Agency said: At 2.50pm yesterday HM Coastguard was alerted to an overdue diver at Scapa Flow.
"Coastguard Rescue Teams from Kirkwell and Stromness, lifeboats from Longhope, Stromness and Hoy and the search and rescue helicopter from Sumburgh carried out an extensive search.
“The search was stood down at 2am today (June 28) pending further information.”
A Police Scotland spokesperson said: "Around 5.35pm on Sunday, 27 June, we were made aware of a diver missing in waters at Scapa Flow, Orkney.
"Police are supporting a multi-agency response as searches continue in the area."