Rescue workers found the car about 7:30 p.m., about 100 feet from where the driver lost control 2½ hours earlier, Houston Fire Assistant Chief Omero Longoria told the Houston Chronicle for its online edition.
The car came to rest in a drainage ditch filled with about 9 feet of water. Two men and a 10-year-old girl managed to escape the car, but a strong storm current initially prevented rescuers from getting to it, Longoria.
Travis Campbell, 24, watched in shock as police and firefighters searched for the bodies of his 7- and 10-year-old nephews.
"At this point, I just want their bodies to be found," Campbell said.
Further information about the occupants of the car was not immediately available.
The children's deaths would bring the weekend death toll to six from the massive storms that moved across southeast Texas.
A 76-year-old Fayette County man died after his car got stuck in a flooded underpass in Schulenburg, midway between Houston and San Antonio. Frank Floyd, 76, of Hallettsville, drowned Friday afternoon after he and his wife became trapped after driving into a flooded railroad underpass on U.S. 77, said Schulenburg Police Chief Randy Mican.
Floyd's wife, Mary, 72, managed to escape and was taken to a hospital. Her injuries were not believed life-threatening, the chief said.
Nearly 5 inches of rain had fallen at Houston's Hobby Airport by 5 p.m. Saturday.
The initial leg of an annual 150-mile charity bike ride involving more than 13,000 cyclists raising money for the National Multiple Sclerosis Society was washed out Saturday by the second consecutive day of heavy rain.
The 25th annual MS 150 had been scheduled for Houston to La Grange. It was scrapped after Friday's torrential rains flooded the Fayette County Fairgrounds, where tents were set up for overnight accommodations for participants. Saturday's continuing downpours made riding treacherous.
Organizers of one of the nation's largest such events hoped clearing weather forecast for Sunday would allow for the second half of the ride from La Grange to Austin.
At least 10 inches of rain fell Friday in Colorado County, about 70 miles west of Houston, closing some roads. Hail measuring 1.75 inches in diameter was reported Friday night in Laredo, along with some street flooding in Zapata County in the Rio Grande Valley.
More heavy rain fell Saturday, and nearly all of East Texas and portions of South Texas were under some kind of threatening weather advisory with tornado warnings and watches and flash flood warnings and watches in place.