Water seeped into the foundation soil under the light-rail tracks, resulting in the tracks settling at the intersection. The rails will be removed and the base excavated and replaced with a different material that will hold up better in wet conditions, Holden said.
HRT will bear the cost, which has not been calculated, he said.
The area near The Hague is known to flood when tides rise abnormally high.
"Flooding occurs in Hampton Roads," Holden said. "The area is formerly known as Tidewater for a reason."
He said that once light-rail service begins a year from now, there could be times when high water shutters the system. He said building an elevated light-rail line was cost- prohibitive.
Holden said inspectors would ensure there are no other settling problems along the 7.4-mile light-rail line that runs from Newtown Road at the city line through downtown to the medical complex on Brambleton Avenue.
"When you build stuff like this and things don't go quite right, you tear it up and redo it," he said.