The Irish Sea, like many marine areas, is threatened by anthropogenic activities. In particular the Pisces Reef system, a series of smothered rocky reefs are subject to fishing pressures as a result of their position within a Nephrops norvegicus fishery. In an area of sediment deposition and retention the reefs modify the environment by increasing the energy of near-bottom currents which results in localised scouring. This is the first study to attempt to characterise and investigate the ecological functioning of the Pisces Reef system. A multidisciplinary approach was essential for accurate investigation of the area. To facil- itate more effective management of the benthic habitats of the Reef system, this study integrates acoustic, seismic, grab sampling and video ground-truthing methods for benthic habitat discrimination. Orientation of the scour hollows also suggest that seabed features could be used to infer dominant flow regimes such as the Irish Sea Gyre. The data revealed significant geology–benthos relationships. A unique biotope was described for the reef habitat and it was demonstrated that scouring may influence community composition through disturbance mechanisms. This study provides preliminary information required for management of a unique habitat within a uniform region.