A small stone structure near the monastic enclosure was recorded in 1996 as a souterrain, the term used for the narrow underground passages, typically dry-laid and roofed with stone lintels, that appear at many early medieval Irish sites and are thought to have served for storage or refuge. The description seemed to fit: a low lintelled opening facing south-east, a passage running westward for just over three metres, roofed with twelve lintels, its northern side cut from living bedrock and its southern wall of drystone construction. It was compact, dim, and clearly purposeful.

What the 1996 survey could not have anticipated was what restoration work would eventually reveal. On closer inspection during that work, the structure was identified not as a souterrain at all but as a cistern, a water-collecting or storage chamber, a distinction with considerable implications for how the monks managed their survival on a rock almost entirely exposed to Atlantic weather. The structure sits approximately eighteen metres west of one of the monastery's beehive cells, known as Clochaun A, and its lintels slope noticeably downward to the south, a feature explained by the partial collapse of the southern side-wall. The clarification came through Edward Bourke, and the structure appears labelled as such in a LiDAR survey of the monastery published by Bourke, Hayden and Lynch in 2011. Fresh water would have been among the most precarious resources on Skellig Michael, and a purpose-built collection chamber, however small, speaks directly to the ingenuity required to sustain monastic life there at all.