A number of important areas have reopened but a spokeswoman said damage to the site's infrastructure could take months to repair.
The railway line between Lourdes and the nearby town of Pau has been washed away, forcing visitors to arrive by bus or on pilgrim trains via Toulouse.
The two cafeterias that feed Lourdes' workers are still shut, as are some hotels.
Local power stations have been shut down, forcing the site to buy expensive electricity from the French national grid.
Further flooding is feared if the snow blocking five nearby mountain passes melts and runs into the river.