The Well of St. Francis is not lost in any dramatic sense; it has simply slipped out of the physical record, surviving only as a boundary marker in a sixteenth-century administrative document, a fixed point on a vanished landscape.

The well appears in Archbishop Allen's Register, a source compiled around 1530, in a passage defining the extent of the Liberty of St. Thomas. The Liberty, a jurisdictional area associated with the Augustinian Abbey of St. Thomas the Martyr, was described as beginning "beyond the island of the Coombe behind the former gallows of the Archbishop, and on this side of the well of St. Francis." That single sentence does considerable work. It places the well in relation to an archbishop's gallows, a detail that speaks to the considerable secular authority held by the medieval church in Dublin, and it names the well after St. Francis, suggesting a connection, however loose, to the Franciscan presence in the city. What the entry cannot tell us, and what researchers including Clarke (2002) and McNeill (1950) have noted, is exactly where along The Coombe this well stood. The "island" mentioned in the register likely refers to a slightly elevated or enclosed piece of ground rather than anything surrounded by water, but the precise geography has not been reconstructed with any confidence.

The Coombe today is a busy urban street running through the Liberties, roughly between Patrick Street and Meath Street. There is nothing to mark the well's former existence, no plaque, no depression in the pavement, no surviving folk memory attached to a particular doorway or corner. For anyone curious enough to walk the street with this history in mind, the absence itself becomes the point. Holy wells in Ireland were typically modest features, a stone surround or a seep of water in a field, which is partly why so many vanished once urban development overtook them. What survives here is a single clause in a church register, enough to confirm that something sacred once occupied this ground, but not enough to say precisely where you are standing in relation to it.