A kayaker traveling along the river west of La Valle found the bodies May 8, according to a news release the Sauk County Sheriff's Department issued Tuesday.
The horses, Jimmy and Vicki, were used in therapy programs for veterans and troubled youth at September Farms in La Valle.
Sauk County Sheriff Chip Meister said it appeared that the horses had drowned by accident in the icy, high river, countering initial suspicion that the animals had been stolen when they went missing in March.
The river flows through the 70-acre farm that is home to nearly 50 rescue horses.
"The investigation has never generated any evidence of criminal activity," Meister told the Baraboo News Republic
Angela Joseph of Dane, who owned the 3-year-old palomino Morgan gelding named Jimmy, told the La Crosse Tribune she has no idea how the horses got to that area of the pasture.
"Things are not making sense. We can't figure out how they got down to the river. Those horses normally didn't hang out together because they're from different herds," Joseph said.
A police officer used the other horse, a 2-year-old chestnut Morgan filly named Vicki, as a therapy animal.
"It's been very traumatic for all of us, getting them out of the water," she said. "It's very disheartening."
"The only good news is we were able to give them a dignified burial," Joseph said.