Avron Adams, 18, of Schertz, and a friend got caught Saturday in the swift waters of Cibolo Creek after about half a dozen friends swam across. One friend held onto a tree branch and got out, but Adams did not, officials said.
David Harris, a spokesman for Schertz, said about 5:45 p.m. searchers located Adams' body near the water's edge. Harris said Adams' family has been notified.
"The body was found near where the search and rescue dogs had identified a scent," Harris said.
Earlier Sunday, Adams' father said he was holding out hope.
"We're hopeful, but at this point, you just don't know," his father, Kenneth Adams, told The Associated Press as his wife stood nearby. "It's very hard. We're just keeping the faith."
The search effort included helicopters, divers and rescue teams in inflatable boats.
The usually dry creek in Schertz, northeast of San Antonio, had dropped about 10 feet since Saturday. Other rivers in the San Antonio area and surrounding counties continued to drop after peaking above the flood stage, but flood warnings remained in effect Sunday. The National Weather Service issued a flash flood watch for seven counties until 6 p.m. Sunday, saying thunderstorms could produce heavy rainfall.
Two women died Saturday after being swept away by floodwaters, some as high as 10 feet on some roads. One who was trapped in her car climbed to the roof before being swept away, and her body was found against a fence, said San Antonio Fire Department spokesman Christian Bove. Emergency officials also recovered the body of a woman in her 60s, whose car was carried away by water as firefighters were trying to rescue her. Authorities did not immediately identify the women who died.
On Sunday, about 20 people were at a shelter set up by the American Red Cross, including some whose apartment complex roof caved in under the weight of the heavy rainfall.
Roxanne DeLeon arrived there Sunday with her 18-month-old son, 6-year-old daughter, 15-year-old daughter and husband, a day after escaping through waist-deep water in their rented home with nothing but what they were wearing, her purse and some diapers. They didn't even have time to grab shoes.
DeLeon said they spent the night on the floor of a relative's home because family members don't have enough room for all of them, and their insurance agent cannot provide help that would get them into a motel or apartment until after Memorial Day.
"It feels like we're stuck," DeLeon said Sunday. "One relative can keep my son part of the day while I'm at work, but who's going to pick up my kids from school? I never thought my family would go through something like this."
The San Antonio International Airport recorded 9.87 inches of rain Saturday, the second-highest official daily rainfall in city history.
Associated Press writer Angela K. Brown in Fort Worth contributed to this report.