The normally tranquil Gave de Pau, the river that runs through Lourdes, burst is banks after heavy rain that has hit the Haute-Pyrénées region since Thursday and muddy water invaded the lower parts of the town.
Pilgrims were transported by coach to a conference hall and a sports hall.
The sanctuaries were closed Saturday and the grotto where Bernadette Soubirous claimed to have seen a vision of the Virgin Mary was under a metre of water.
About 40 people were moved from their homes in the nearby village of Pierrefitte-Nestelas on Saturday morning and two camp sites at Cauterets were evacuated.
Three roads in the area were closed.
High winds on Thursday and Friday caused electricity to be cut off from about 8,000 households in the south-west. The electricity supplier, EDF, promised to restore the supply by Saturday evening.
More heavy rain was expected on Saturday night.