During the middle ages, monasteries used water for the preparation of food, for sanitation, for rituals and also for industrial production. For these purposes monks or their workmen dug wells and tunnelled into hillsides to locate sources of water. They diverted streams and built complex conduit systems in order to bring fresh water to their site. They also constructed interconnected drains and large sewers to remove used and excess water from their precincts. Study of the ways in which a monastery managed its water resources thus touches on many aspects of its ritual and daily life.

Study of Saint-Jean's water management system reveals four major phases of development and modification over the course of the nearly one thousand year history of the site. Of the first phase at Saint-Jean, extending from the foundation to c.1200, the information recovered is limited and suggests that water management on site was relatively modest in scope and rather traditional. As we will see, however, the earliest phase of the abbey’s water management is best documented off-site in the Crise river valley where the community had mills and a fishpond.

The second, thirteenth-century phase completely transformed the earlier system and was decisive for water management throughout the rest of the abbey's history. This new system included a new, nearly two kilometer-long siphon-powered aqueduct that brought fresh water to the site as well as extensive, stone-built sewers to remove used water from the precincts. Saint-Jean is among the four or five medieval monastic sites known to have been engaged in long-distance siphon engineering during the late eleventh, twelfth and thirteenth centuries.

The third phase of water management at Saint-Jean-des-Vignes, corresponding to the Catholic Reformation, transformed this liturgical and functional system into a decorative and functional one.

By c.1230 at the latest, the canons of Saint-Jean-des-Vignes possessed two springs. The first spring is not mentioned in any medieval or post-medieval document known to us. That spring, however, is, however, still visible as an outdoor fountain located about 100 meters to the west of the abbey, within the precincts of the former military base opposite the Gothic façade. It may have been in the abbey’s possession from its foundation.

Charter evidence suggests that, sometime before 1230, the canons acquired a second, more powerful, spring located nearly 2 kilometers southeast of the precincts, at the foot of Mont Sainte-Geneviève. During the next two decades an aqueduct was constructed to bring its fresh water into the abbey for the kitchen, for the lavabo in the cloister and perhaps for the garden zone east of the claustral buildings. New vaulted sewers, one of them integral with the new latrines and flushed by water from the old spring, were also constructed to evacuate used and excess rainwater.