The Blue Mountains water skink Eulamprus leuraensis is an Endangered swamp specialist known from < 60 sites and restricted to the rare, threatened and fragmented habitat of Temperate Highland Peat Swamps on Sandstone. Understanding the species’ ecology, notably its vulnerability to threatening processes such as hydrological disturbance, is essential if we are to retain viable populations of this Endangered reptile. We examined the impact of anthropogenic disturbance (longwall mining practices, development (industrial, urban, infrastructural) and damage by recreational vehicles) on this species, other herpetofauna and the swamp by surveying six paired undisturbed and disturbed sites in south-eastern Australia. The abundance of E. leuraensis was severely affected by disturbance. The species was absent from disturbed swamps, where it was replaced by its congener E. heatwolei and other woodland reptile species. Disturbance was associated with a halving of soil moisture content and a loss of surface water; the dense, live understorey was replaced by a sparser, drier habitat with dead vegetation, logs, rocks and bare ground. In effect, disturbance eliminated the distinctive features of the swamp habitat, transforming it into an area that resembled the surrounding habitat in terms of fauna, flora and physical characteristics. Our surveys suggest that hydrological disturbance (groundwater loss or alterations in surface water chemistry) extirpates E. leuraensis. This species' dependence on groundwater renders it sensitive to habitat degradation through hydrological disturbance. The conservation message for management authorities is clear: to protect the skink, protect the habitat.