Workers cut a rectangular pit, roughly 3.8 metres east to west and just under 2 metres north to south, directly through sandstone bedrock to a depth of 1.4 metres, then constructed the mill inside this excavated undercroft. It is an unusual approach: rather than fixing the upright structural posts to base plates at ground level, as was standard practice, the builders cut sockets into the bedrock floor itself and seated the posts directly in them. The sides of the timber structure were planked, and the gap between the planking and the rock walls was packed with stone and clay, making the whole thing something between a built structure and a fitted lining.

What survives tells a precise story. Part of the flume, the channel that directed water onto the horizontal wheel below, was recovered in a badly degraded state, along with the beam that supported it and two substantial timbers running along the north and south sides of the undercroft. A horizontal-wheeled mill, unlike the vertical waterwheel most people picture, used a wheel mounted flat on a vertical axle, spun directly by water channelled at it from below; the technology was widespread in early medieval Ireland before gradually falling out of use. Sixty-nine timbers were examined in total, sixty-three of them oak, the rest ash, hazel and willow. The base of one rectangular post survived in place, showing both saw and axe marks. Two objects were also found: a fragment of a large millstone and a copper alloy stick pin of a type comparable to pins recovered from thirteenth and fourteenth century excavations in Cork city. The flume support beam, dated by dendrochronology, the science of reading tree-ring sequences to establish felling dates, came back at AD 1150, plus or minus nine years. That single date places the Ballythomas mill among the latest known horizontal-wheeled mills in Ireland, at a point when the technology was already giving way to other forms.