Divers found Devon Morrison's body at about 12:30 p.m. near the Ashfield Street bridge in Belding, Belding Police Chief Dale Nelson said at a news conference.
"We're all upset about it," Nelson said. "We expected a better outcome." He said Devon was a "great kid" and said he was honored to have known him.
Nelson declined to say whether the boy's death was accidental, pending an autopsy and "taking care of evidence."
"Please keep his family and thoughts in your prayers," the city posted on its Facebook page.
Nelson said there are no suspects in the case.
"It's just tying up all the loose ends," he said.
The Belding boy was last seen Saturday as he headed for the Flat River with a fishing pole. He was a fifth-grader at Woodview Elementary School.
Police said Devon would regularly fish alone at the river, which is about 700 feet from his home.
Authorities searched the river, about 25 miles northeast of Grand Rapids, on Sunday with boats and helicopters.
The area near the Ashfield Street bridge was searched extensively Sunday. Shoes were found in the river at about 2:30 a.m. Sunday, and Devon's fishing pole was found Monday.
"I believe in our initial search, we did everything we could do given the conditions and the available personnel," Nelson said.
Rachel Satterlee of Belding, who helped in Sunday's search, said she was having a bad day about two weeks ago when she met Devon briefly.
"Here was this kid walking by me with a fishing pole. I asked him if the fishing was good. I expected him to walk past without saying anything," she said. "But he didn't. He stopped and put his hand on his hip and said, 'No, not today.'"
Satterlee said Devon then proceeded to tell her the reasons why the fishing was poor and that he hoped to have better luck next time. It left her with a smile on her face, she said.