Authorities were searching for at least two other people one who went missing after being trapped in another car and a teenage boy who was swept away while trying to cross the swollen Cibolow Creek in suburban Schertz.
The Fire Department conducted more than 235 rescues across the city, some by inflatable boats, authorities said. They continued their search into the evening.
"We'll be out there as long as daylight permits and again in the morning if the water recedes," San Antonio Fire Chief Charles Hood said, adding that going into floodwaters was more dangerous for firefighters than entering a burning building.
By nightfall, water still pooled in ditches and underpasses. Several roadways were closed, including a major highway that links the suburbs and the city.
But even in low-lying neighborhoods along Commerce Street east of downtown a faded stretch of clapboard houses and beauty parlors yards were clear. In the tourist district around the River Walk, the streets were thick with weekend revelers.
While the water in some homes rose 4 feet high, according to Bove, most residents experienced the floods primarily as a major traffic hassle. Karen Herring, 50, who spent the day volunteering at a fitness contest at the AT&T Center, said participants complained of three-hour drives across town.
Brent Rose, 39, a law enforcement officer who drove in for the contest from the semi-rural northern suburbs, said the damage extended beyond the city.
"We had some fences rolled over by the water," Rose said. "Some farm animals went astray. But not a big deal."
In the city, even a municipal bus was swept away, but firefighters on a boat were able to rescue the three passengers and driver, public transit spokeswoman Priscilla Ingle said. Nobody was injured.
The San Antonio International Airport by Saturday afternoon had recorded 9.87 inches of rain since midnight, causing nearly all streams and rivers to experience extraordinary flooding. The highest amount of rainfall recorded since midnight was 15.5 inches at Olmos Creek at Dresden Drive.
Mayor Julian Castro urged residents not to drive.
"We have had too many folks who continue to ignore low-water warnings," Castro said at a Saturday afternoon news conference.
A flash flood warning was issued for nearly two dozen counties, with up to 4 inches of rainfall forecast overnight.
A flood warning remained for Leon Creek at Interstate 35, where the level was 27.1 feet and was expected to peak at 29 feet Saturday night nearly twice the flood stage of 15 feet, according to the National Weather Service. The San Antonio River about 20 miles southeast of the city, near Elmendorf, was expected to peak at 62 feet by Sunday morning, well above the flood stage of 35 feet.
The National Weather Service compared the flooding to the storm of October 1998, when 30 inches of rain fell in a two-day period. In that flood, the Guadalupe and San Antonio River basins overflowed, leaving more than 30 people dead, according to the Guadalupe-Blanco River Authority.
Due to that history, Hinojosa said, residents were prepared, despite the storm's pace.
"We've been through floods before," he said.
Associated Press writers Angela K. Brown in Fort Worth and Danny Robbins in Dallas contributed to this report.