Stanislaus County Sheriff Adam Christianson said the body, which was found near Santa Nella, is that of Juliani Cardenas.
Police have been combing the canal for weeks searching for Cardenas and kidnapping suspect, Jose Rodriguez, who is the ex-boyfriend of the child's mother.
Rodriguez's Toyota Corolla was pulled from the bottom of a nearby canal on Friday with no signs of Cardenas or Rodriguez inside.
Authorities said Cardenas' body was spotted by a water department worker around 7:30 a.m. about 30 miles downstream from the car.
Christianson say a homicide warrant has been issued against Rodriguez, but investigators believe the man's body also will be found in the canal.
The Associated Press contributed to this report.