Thousands of pilgrims were evacuated from hotels and given shelter in a conference center and sports center, Radio France Internationale reported. The lower part of the small market town was flooded, with about 3 feet of water covering the grotto floor.
The Gave de Pau, the river that passes through Lourdes, flooded after two days of heavy rain in the Haute Pyrenees. More rain was forecast for late Saturday.
Lourdes, with a spring many Catholics believe has miraculous healing properties, has about 15,000 residents and is visited by millions of people every year during the March to October pilgrimage season.
The shrine dates back to the 19th century and is where Bernadette Soubirous, a miller's daughter, reported seeing visions of the Virgin Mary in 1858.