The 13-year-old boy went missing on Monday after he went underwater and did not resurface near Washington Park Beach.
The boy was from Michigan City, Indiana Conservation Ofc. Alex Neel said.
He was found in about 11 feet of water on the east side of the pier where he went missing.
Ofc. Neel said nobody should have been swimming in the water that day due to the rough conditions.
Drone video recorded around the time the boy went missing shows choppy water and waves slamming into a lighthouse pier.
According to a photographer, the boy had been with a small group of children wading in just a few feet of water near the pier minutes before he went under.
On Wednesday morning, DNR officials confirmed they found the boy's body in Lake Michigan.
Officials have not released the boy's identity.
During the initial response, four divers were hurt while searching for the boy. Officials said they were treated for minor injuries.
No foul play is suspected.