The Mendocino County Sheriff's Office said the initial discovery was made on Sunday, as searchers were scouring the Eel River in Legget, California.
The bodies of all four members of the missing Thottapilly family from South California have been found by search and rescue teams.
The family was on a road trip to Portland, Oregon and coming back to their home in California, when they went missing.
The vehicle was encased in sediment and visibility was poor but divers believed there was at least one body inside, officials said.
The boy's mother, Soumya Thottapilly, 38, was found Friday miles from the crash site in an area previously covered with water from the storm-swollen river. Sheriff Allman announced that earlier that morning search crews had located a female body in the Eel River approximately 7 miles north of the collision scene.More news: Greens want to legalise cannabis for adult use
More news: Russian FM calls attacks on Syria unacceptable
More news: Miami Heat look to even playoff series
The body has been identified as that of 12-year-old Sidhhanty Thottapilly. Sandeep Thottapilly (41), Soumya Thottapilly (38), Siddhant Thottapilly (12) and Saachi Thottapilly (9) went missing after the vehicle in which the family was travelling fell into the river on April 6.
An inter-agency search and rescue team has recovered two more bodies of an Indian American family who were feared drowned in a California river some 10 days ago, U.S. officials said on Tuesday.
"An autopsy is expected to be performed this week as part of the Coroner's investigation into the incident", it added.
Before the family was known to be missing, authorities in Mendocino County received reports that a vehicle southbound on US 101 went off the highway and tumbled into the Eel River. They had been travelling south from OR along Highway 101 when the incident occurred, officials said. Authorities said they found "various personal items consistent with a family travelling on vacation" during the course of the two-day search. Sandeep, Soumya, Siddhant, and Saachi were last seen in Klamath, in Del Norte County on April 5.