Beneath the ground floor of Maynooth Castle's keep, excavators found not one well but two, one sealed inside the other's history. The first was infilled, most likely when the ground floor was extensively remodelled in the early 15th century, and a replacement was then sunk nearby in the same western half of the keep. Two wells, occupying roughly the same space across different generations, is a small detail that points to something larger: a site so continuously and intensively used that even its water supply was rebuilt and buried over.

The 1996 excavation, carried out by Dúchas, The Heritage Service, ahead of the conversion of the keep's ground floor into an exhibition space, revealed seven distinct phases of occupation compressed into a single interior. The stratigraphic sequence runs from a rectangular prehistoric building, associated with a stone axe head and an unfinished macehead found nearby, through at least two early medieval post-and-wattle round houses, each roughly 5 metres in diameter, whose hearths yielded good carbon samples though no datable objects. The site appears to have passed into Norman hands around 1175. The earliest Anglo-Norman evidence is a low sod mound, about a metre high, topped by a rectangular post-and-wattle building within a fenced enclosure; finds from this level included an arrowhead, an iron spur, and a scabbard chape, along with Ham Green ware pottery. The stone keep itself was probably first built in the late 1180s, its construction marked by thick mortar slicks across the floor. The 15th-century alterations introduced two wicker-centred barrel vaults, a roofing technique in which wicker formwork supported the arch while the masonry set, supported on a new spine wall threading between the original piers. It was during or shortly after this phase that the first well was abandoned and the second opened. The keep remained in use until the Silken Thomas Rebellion of the 1530s, when it was badly damaged.