Notre Dame des Marais is home to two organs. A 19th century choir organ and the nave grand organ, built in the 16th century composed of two parts.

The lower part of the case of the nave grand organ, known as « cul-de-lampe », was made in 1501 by Evrard Baudot and displays rich sculptures in the flamboyant gothic manner.

The higher part, with its pipes in the Renaissance style, dates back to the 1530’s and was made by Sainctot Chemin.

 Today’s instrument is a small organ in the French style, praised for its sound. It was restored in the 1980’s and inaugurated in March 1984 by the famous French organist Marie-Claire Alain.