Black Hawk County Sheriff's Capt. Rick Abben gave few details about the find, The Des Moines Register reported. He said the identities need to be confirmed.
But he said the families of Lyric Cook-Morrissey and Elizabeth Collins were told of the discovery.
"It's definitely not the outcome that we wanted, obviously," Abben said.
The cousins have not been seen since they went on a bicycle ride July 13. Their bikes were found near Meyers Lake, but an extensive search through the countryside and examination of car trunks and seats found no sign of them.
Lyric was 10 and her cousin 8 at the time.
Carrie Yu of Elk Run Heights, whose son was at the same elementary school as Elizabeth, was one of about 50 people at a candlelight vigil Wednesday night near Meyers Lake. Yu helped search for the girls after their disappearance and was hopeful they would still be found alive.
"We're still holding out complete hope that it's not them," she told the Register.
A reward for information in the case grew to $150,000 recently when an anonymous donor added $100,000.