Rescue services Director Patrick Heyraud told the regional La Depeche du Midi newspaper there was still as much as 3 feet of water in the city, but levels were subsiding.
"That means that we begin our work pumping out cellars and basements, pump out the water that is in low-lying areas and in the shrines," he said.
Saturday, some 400 religious pilgrims were evacuated to higher ground as the Gave de Pau River rose, Radio France International said.
The river level was forecast to fall throughout Sunday, the report said.
There was no immediate report on the cost of damage.
The heavy rains began this week in Spain to the west and have caused at least one death there, RFI said.