The body of 3-year-old Breeann Rodriguez was found in a drainage ditch on Tuesday.
"We are saddened to confirm our fears but glad we have been able to recover her for her parents," Senath, Missouri sheriff Bob Holder said in a statement.
The body was found in a remote floodway eight miles from her home in Senath, the Associated Press reported.
A Missouri State Highway Patrol officer was searching by boat and found the body on the bank of a drainage ditch, the Dunklin County sheriff's department said on Wednesday.
Breeann went missing on Aug. 6. She was riding her bicycle outside of her house with her 5-year-old brother. He went inside for a moment and when he came out she was gone.
A week later, police arrested a suspect, neighbor Shawn Morgan. Morgan said he found Breeann standing on his pool ladder in his backyard. He said he grabbed her, took her inside, and suffocated her with a garbage bag.
He also said he dumped her body over a railing into a river system.
His motive, however, remains unclear.
"It's all a mystery," Crowder said.
Breeann's funeral is scheduled for Saturday afternoon at the Senath Church of Christ, the AP reported.