The Mendocino County Sheriff's Office said the initial discovery was made on Sunday, as searchers were scouring the Eel River in Legget, California.
Around 11:30 a.m., a team of searchers on a boat noticed a gasoline smell coming from the water approximately half a mile north of the site where the Thottapilly family's car was reported to have crashed. The searchers found a vehicle submerged around 4-6 feet beneath the water, officials said.
The vehicle was encased in a large amount of sediment from the river current, and it took hours for the car to be towed out of the water.
Sheriff's officials confirmed that after the car was out of the river, searchers were able to recover the bodies of Sandeep Thottapilly, 42, and Saachi Thottapilly, 9, from inside the car.
On Friday, the body of a woman was recovered about 7 miles north of the reported crash site. Coroner's officials were later able to identify that individual as Soumya Thottapilly, 38.
Later Monday around 4 p.m., officials said they removed the body of a boy from the water about six miles north of the crash and identified him as 12-year-old Siddhant Thottapilly.
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The California Highway Patrol does not believe there is any foul play.
"The vehicle attempted to pull over to the shoulder into a big pullout, and the vehicle came close to coming to a stop and ended up going over the edge and into the river," said Lt. Randy England of the California Highway Patrol.
Last week, investigators found personal items belonging to the Thottapilly family in the Eel River.
Authorities said they found "various personal items consistent with a family traveling on vacation" during the course of the two-day search. Relatives of the Thottapilly family positively identified the items as belongings of their family members, authorities said.
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The family was scheduled to arrive to visit a friend in the San Jose area on April 6 as a strong storm dumped rain on Northern California, but never showed up, authorities said. Sandeep, Soumya, Siddhant, and Saachi were last seen in Klamath, in Del Norte County on April 5. They were reported missing on April 8.
A witness recalled seeing an SUV matching the description of the missing Valencia family's vehicle plunge into the Eel River.
The Associated Press contributed to this report.