Ouray (yoo-RAY') County authorities say a remote-controlled rover and divers working in cold, murky waters spotted the bodies.
The wreckage will have to be brought to shore before the bodies can be removed, authorities said. They say the plane is upside down in about 3 feet of silt and about 60 or 70 feet underwater.
A salvage team is expected to begin raising the wreckage on Wednesday.
Authorities haven't released the identities of the victims.
The single-engine Socata TBM took off from Gadsden, Ala., and was headed to Montrose, about 25 miles north of the reservoir, when it crashed into the water at Ridgway State Park on Saturday.
The flight stopped in Bartlesville, Okla., before continuing on to Montrose, Federal Aviation Administration spokesman Ian Gregor said. The cause of the crash isn't yet known.
According to preliminary reports, the pilot reported that the plane was in a spin before losing communication, National Transportation Safety Board spokesman Eric Weiss said Monday.
That's consistent with an eyewitness account from a woman who was attending a wedding nearby when the plane crashed.
"It popped out of the thick, heavy clouds and went into a flat spin," Lena Martinez told the Ouray County Plaindealer.
Such eyewitness accounts have been turned over to the FAA and the NTSB for their investigations.
The plane is registered to an Alabama corporation. Messages left for the company weren't immediately returned.
The crash occurred several weeks after three people died when a plane crashed after taking off from the Telluride airport, less than 50 miles south.