"The flood's recession has been clearly confirmed," the prefect's office for the Pyrenees-Atlantiques region said in a statement.
Many roads remained closed however and some residents were still unable to return to their homes.
The floods this week sent water pouring into the religious sites at Lourdes, forcing thousands of tourists to be evacuated and suspending visits.
Lourdes, where the Virgin Mary is said to have appeared to a local peasant girl in 1858, is visited by six million people every year, with the numbers in July and August peaking at up to 40,000 a day.
Officials said 37 hotels in the town were badly damaged by the floods and would not re-open for several months.
The grotto had been due to reopen but authorities said this was being pushed back to .
The underground Basilica of Saint Pius X, which can normally host up to 25,000 pilgrims, remained partly flooded, with its floor covered by mud.
Officials said more than 300 calls had come in offering donations to help with repairs.
Flooding last October caused an estimated 1.3 million euros in damages to Lourdes but the clean-up operation is expected to be significantly more expensive this time.
Three people were killed in the flooding, including a 54-year-old woman found drowned in her car and two elderly people swept away by the waters.