Chunks of the building were ripped off and water poured down the steps at one end of the seating area, flooding the floor around the competition pool Friday.
Superstar Michael Phelps and hundreds of swimmers were ordered out of the water and into interior hallways, cutting short their workouts. The building was later closed for the night to assess damage and make repairs in time for Sunday's start of the eight-day trials.
There was no structural damage, although the arena lost insulation and sustained water damage, building spokeswoman Rebecca Kleeman said.
"Really ominous, that's for sure," said two-time Olympian Erik Vendt, who, along with Phelps, was walking from their hotel to the arena when tornado sirens sounded.
Hail, heavy rain and wind of at least 50 mph tore through the city during the storm.
On a lighter note, Vendt joked that the storm might have been a good omen.
"When we came into the 2000 trials in Indianapolis, the same type thing happened," he recalled. "Just a crazy thunderstorm that shook the hotel. Maybe that's a good sign. USA Swimming puts us in tornado alley during tornado season."
Phelps is entered in a staggering nine events during the meet, though he'll likely drop at least two or three of them at some point. But he will surely attempt to qualify in at least five individual events, which, when combined with three relays, would give him a second shot at Mark Spitz's record of seven gold medals at the 1972 Munich Olympics.
Four years ago, Phelps came up just short: six golds and two bronzes.
He holds the world record in four of his planned events: 200-meter butterfly, 200 freestyle and both the 200 and 400 individual medleys. He's also entered in the 100 fly, 100 and 200 backstrokes, and 100 and 400 free.
Don't expect him to swim them all.
"He's obviously entered in more events than he will swim," coach Bob Bowman said. "We'll just take it day by day which ones he will swim. Maybe he will only swim the prelims or semifinals of some, just to get a feel for those events."
While all eyes are sure to be on Phelps any time he dives in the water, there's plenty of compelling stories among the 1,250 swimmers who'll be competing for a maximum of 52 spots on the U.S. team.
Katie Hoff is the workhorse of the women's events. The 19-year-old from the same North Baltimore club that produced Phelps is entered in seven and plans to swim at least five.
Hoff shrugged off any comparisons to Phelps, but she's clearly not bashful about taking on the same sort of workload. She definitely plans to swim the 100, 200 and 800 free, the 200 and 400 medleys and quite possibly the 200 back.
"I like swimming a lot of events," she said. "It helps spread the nervous energy out over several events rather than just one."