Officials at the Qwest Center near downtown Omaha closed the building to examine it after superstar swimmer Michael Phelps and hundreds of other athletes were herded into hallways because of a tornado warning.
Water poured into the building, down arena steps and onto the deck of the competition pool during the storm. The storm's winds may have reached 100 mph in some areas, said meteorologist Bryon Miller.
An eight-day meet to decide the U.S. Olympic swimming team opens Sunday. Al Berndt, assistant director of the Nebraska Emergency Management Agency, said the damage appeared to be reparable and probably wouldn't halt the swim trials.
Across the Missouri River in Council Bluffs, Iowa, two people died when a tree fell on the car they were in, said Police Sgt. Jason Bailey.
Damage reports in the region included toppled trees and power lines and hail the size of baseballs. Flash flood watches were issued across Iowa, where flooding has been a problem recently.
Berndt said no serious injuries were immediately reported in Omaha, but there were reports of a few house fires caused by lightning.
Hundreds of people had gathered for a 6 p.m. outdoor concert in Omaha and for an arts festival in downtown Omaha. Booths flipped over, and awnings and other covers were whipped away by strong winds.
The outdoor concert and fireworks at Memorial Park was canceled.
A spokesman for the Omaha Public Power District said more than a third of its customers were without power. The district serves 330,000 customers. There were widespread power failures in Council Bluffs, and Bailey said the police department was on auxiliary power.