The sanctuary ringing the cave at Lourdes, whose spring water many Catholics believe can miraculously cure illness was shut by French authorities after which about 200 people were evacuated due to flash floods.
The preventive measure came a day after heavy rain and even some snowfall in the area led to rivers flowing well above their normal levels, even cutting off some roads.
"The Sanctuaries are closed apart from the Upper Basilica," or a Gothic church above the grotto, the local prefecture of the Haute-Garonne area said in a statement.
"We are very vigilant although for the present the situation is not catastrophic."
Local officials said most of the 200 people moved were those camping in the area.
In 2012, the Lourdes shrines were closed after flash floods that caused hundreds of thousands of euros in damage.
Hundreds of pilgrims come to the famous grotto where the Virgin Mary reportedly appeared to a peasant girl in 1858 and whose water many believe has curative powers.