The removal of water formed another aspect of the hydraulic system within the precincts of Saint-Jean-des-Vignes. Today, two underground galleries, datable to the thirteenth century on textual and stratigraphic evidence, survive intact on the site. These galleries served as sewers, one beginning at the lavabo in the middle of the cloister, the other beginning at the toilets at the southern end of the dormitory. At various intervals, the vaults of each of these sewers open into "chimneys" which served as collectors for underground drains nearer to the surface. This feature reveals that the sewers were not simply constructed to remove used water from the site but also to assist the evacuation of excess rain water.

The two sewers are both constructed of hard limestone and vary in height, in width and in form. The interior height of the sewers ranges between 1.10 and 2.15 meters in different sectors. Their widths vary between 45 centimeters and more than a meter, with the sewer beginning at the latrines being the widest. Presumably this greater width is given by the width of the latrines where the sewer begins. It may also have been necessary for efficient flushing, given the greater quantity of water and waste moving through it and the related need to facilitate cleaning. The height and profile on the interiors change a number of times along their lengths. Sometimes linked to different construction phases in older scholarship, these changes are practically motivated, reflecting the presence or absence of buildings overhead, or the need to increase or slow the speed of water. For example, the profile of both sewers approaches a circle where the two systems join just outside the precinct wall in order to increase speed for the descent toward the Crise river where the sewer discharged.

Local tradition holds that the souterrains of Saint-Jean-des-Vignes were used by the canons to escape from the abbey during the Hueguenot sack or the French Revolution. These legends would have the canons following the underground sewers as far as to the cathedral, or even under the Aisne River to the abbey of Saint-Medard. These tradtitions are an exaggeration, although the canons might have used the sewers to escape outside the monastic precinct in the sack of 1567, exiting upward through the aeriation chimneys.