In spite of the precautions taken at the time of the original construction and indicated in 1903 by Alfred Picard, in charge of the 1900 Universal Exhibition, structural disorders soon appeared in the edifice. Before World War II, there had already been several campaigns of engineering work below ground level but subsequent development of the Paris metro, express roadways along the banks of the Seine and the RER underground express rail network altered the level of the water table, leaving the tops of the wooden piles that supported the building exposed to air. No longer protected by water, the piles had started to rot, causing the building to subside. The southern part of the Nave, the most heavily affected, had fallen by 6 inches.
The most urgent work consisted of giving the building a sounder basis on deep foundations resting on hard ground at a depth of 50 to 60 feet. To do this, two techniques were used. For the more critical southern part, now resting on rotting oak piles, moulded walls were built. The sections of the foundation that had no piles were consolidated by 1,850 columns of jet grouting, injections of cement at very high pressure. The work lasted from November 2001 to August 2004.