Extensive land clearing for agriculture in south-west Western Australia has led to highly fragmented patches of remnant vegetation. In this landscape, the fringing vegetation of lakes has an important conservation priority in a biologically diverse region but is vulnerable to altered hydrological regimes and easily degraded by waterlogging and salinity. Protection of the fringing vegetation with direct intervention approaches such as drainage or pumping schemes requires knowledge of the tolerance or ‘coping’ range of species targeted for conservation. To obtain this information the health of vegetation in relation to waterlogging and salinity is assessed in two lake systems north of Esperance in south-western Australia. The lower reaches of both systems are dominated by healthy halophytic species. Mesophytes, phreatophytes, xerophytes, and combinations of these classes dominate the upper reaches but are mostly degraded. There are unhealthy and healthy pockets of mesophytic, phreatophytic, xerophytic species, and combinations of these classes occurring at similar elevations above shallow groundwater, indicating that temporal hydroperiod thresholds are important for these species.