The deputy was walking along the beach shortly after 7 a.m. Saturday, when he saw the body in the water just off the beach, said Lt. Steve Kempker.
The body matched the description of John English, 47, who disappeared on June 30, when he jumped into the water to go for a swim.
Medical examiners confirmed the man's identity during an autopsy conducted Saturday afternoon at Sparrow Hospital in Lansing, Kempker said.
The cause of death is still undetermined pending the autopsy results, he said.
The private boat stopped north of the Grand Haven pier heads about 4 p.m. that Sunday so the man could swim.
Although the day was hot, the temperature of the lake was still very cold,
Police said at the time, English's friends on the boat could tell he was immediately in distress.
The boat was drifting away from the swimmer and efforts to throw the man life rings were futile as he slipped below the surface.
Crews from the Coast Guard, Ottawa County Sheriff's Department Marine Patrol, Norton Shores Emergency Services, the Muskegon County Sheriff's Department and Michigan State Police searched the waters for three days, but were unable to recover the man's body.