After the water level had receded, the pilgrimage site was cleaned and reopened to visitors on Saturday evening, the pilgrimage site announced on its website.
The Chapel of Lights, which was also flooded, should be open to the public again on Sunday.
According to the information provided, the baths with the spring water, which is said to have healing properties, remain closed for the time being. They first had to be cleaned and checked after the floods, it was said. They are expected to reopen in a few days.
Pope Francis spoke about the situation in Lourdes during his current trip on Sunday after a mass in Papua New Guinea. "Our thoughts are with the shrine of Lourdes, which has unfortunately been hit by flooding," he said.
The river Gave de Pau, which runs through Lourdes, burst its banks on Saturday after heavy rainfall.
The place of pilgrimage published photos showing the grotto partially under water.
However, the emergency plan for flood protection had "proven its effectiveness", it said.
The French newspaper "La Croix" reported on the evacuation of hundreds of pilgrims from hotels that were threatened by the floods.
The pilgrimage site of Lourdes has already been hit several times in recent decades by floods, some of which were severe.
The grotto on the north side of the shrine, in the immediate vicinity of which the Gave de Pau river runs, has been particularly frequently affected.
Lourdes is one of the most famous places of pilgrimage in the world. In 1858, the 14-year-old shepherd girl Bernadette Soubirous (1844-1879) is said to have appeared to Mary a total of 18 times in the small town in the south of France.
In 1862, the Marian apparition was officially recognised by the Catholic Church. Millions of people from all over the world make a pilgrimage to Lourdes every year.
It was only at the end of May that the media reported on an inexplicable healing in the Marian town.
According to the report, a visually impaired woman from Madrid explained that she had regained her sight during a recent pilgrimage after drinking water from the spring there.