A 70-year-old drowned in an attempt to leave her car in the village of Pierrefitte-Nestalas on Tuesday night, while a 75-year-old man died Wednesday in Luz-Saint-Sauveur.
French officials placed several areas near the Pyrenees mountain range on "red alert," as severe weather raged across the area.
The flooding prompted the closure of the sanctuary at Lourdes, a famous pilgrimage site for Catholics, France 24 reported. Water from the site is believed to have healing power.
"We are very vigilant although for the present the situation is not catastrophic," local authorities said in a statement.
A Lourdes rep told The Local that the shrine was in danger of serious damage.
"It's very serious, the water is still rising. There is nothing we can do. We just have to wait and cross our fingers and hope," he said.
In the video above, water from the Gave de Pau river bursts through the town of Soulom.
Local residents described the scene:
"There's trees and debris strewn everywhere, the car park has been turned into a river and people are getting piggy backed out," a hotel owner said.
"I was up to my chest in water when I returned to the hotel. The water has come into the dining room, all the hotels are affected. We had only just reopened in April after the floods in October," he added.