Onslow County Hans Miller said dive teams found Mariah Miller's body around 5:30 p.m. Saturday.
FBI spokeswoman Shelley Lynch said in a statement the body was in a Pender County creek about 25 miles (40 kilometers) from Mariah Woods' home in Jacksonville.
Miller didn't release any other details at a news conference.
Deputies have charged 32-year-old Earl Kimrey with concealing a death. Arrest warrants say Kimrey moved Mariah's body from where she died, knowing her death was not natural. They haven't said how they think the girl was killed.
Kimrey was living with the girl's mother.
He is being held in the Onslow County Detention Center under a $1,010,000 bond. District Attorney Ernie Lee has been consulted on the current charges and additional charges could be pending as the investigation continues.
On Friday morning, the search for 3-year-old Mariah intensified with a renewed effort that included hundreds of volunteers.
The search was organized by Team Adam, a program for the National Center for Missing & Exploited Children that provides on-site assistance to law enforcement agencies and families in cases of missing children, according to Onslow County Sheriff Hans Miller.
The search for Mariah entered a fifth day Friday. Her disappearance Monday prompted an Amber Alert that has gained national attention.
Authorities searching for the missing toddler asked residents to comb through their properties for anything "out of the ordinary" in the hope that someone would come forward with information that led them to the little girl.
Dozens from the shaken community surrounding Mariah's home turned out Wednesday night for a special prayer vigil at Folkstone Original Freewill Baptist Church. Some of the toddler's extended family members are members of the church.
"They're having some rough moments," said Cliff Wilson, Folkstone's pastor. "They're doing all that they can do and they feel helpless. As a small community that we are, we got to all stick together in this."
Earlier Wednesday, the FBI released surveillance photos of a woman and a little girl who matched Mariah's description, in hopes of identifying the pair.
The FBI later said the woman in the picture did not have any connection to their ongoing investigation to find Mariah.
WCTI spoke with a 23-year-old Newport, North Carolina woman Wednesday who said she was the woman pictured in the surveillance photos.
Jetta Long revealed that her daughter was born with a shortened leg, so she said she understood how her little girl could have been mistaken for the missing toddler.
Mariah's family has said that the 3-year-old struggles to get around on her own and wears leg braces for assistance.
Mariah has been missing since Sunday night when her mother put her to bed.
Woods lives with her mother and her mother's live-in boyfriend on Dawson Cabin Road in Jacksonville, North Carolina.
Her biological father Alex Woods told WCTI 12 Tuesday that he found out his daughter was missing when the Amber Alert was issued and he hasn't seen her for about a year. He said he doesn't believe his daughter was abducted.
WATCH: Raw video of emotional interview with Mariah's biological father
"Someone just walked right up in there, grabbed the 3-year-old out of the bed and she didn't cry, she didn't scream?" Alex Woods said. "Nobody heard anything? Four people in the house, two adults and two kids, someone just comes up and snatches the baby and walks out?"
ABC News reports that her mother reached out to the public in an emotion-filled plea Monday.
"Please, bring her back ... She's my baby, she's my everything," said Kristy Woods in a press conference. "(I) just to be able to touch her and hold her and not let her go again. I'd give anything."
She is described as a white female standing about 2' 9" tall and weighing around 30 pounds. Mariah has brown hair and blue eyes.
The FBI is assisting state and local law enforcement with the investigation; they have brought in the Child Abduction Rapid Deployment for further assistance.
Marines based at nearby Camp Lejeune are also assisting in the search.
Authorities said they have been using all means necessary to find Mariah including ground searches assist by a helicopter and K9 units - so far, officials have covered 100 acres.
Officials said more than 225 state and federal personnel are working on the case, adding that they have conducted nearly 100 interviews and followed up on more than 140 leads.