Billabongs are diverse and productive elements of riverine landscapes, and likely play an important functional role as refugia in these highly variable environments. There is strong historical evidence that billabongs have been negatively affected by a range of human activities, including catchment disturbance and river regulation. Improved catchment management and the delivery of environmental water have the potential to mitigate the negative effects of land use and hydrological changes, however, the effectiveness of these measures will require a good understanding of what the critical stressors are and of how and why their influence might vary within the diverse array of billabongs that exists across riverine landscapes. Many palaeo records from the Murray-Darling Basin show evidence of abrupt loss of submerged plants associated with the beginning of European occupation, however, this change is not consistent and there is evidence of a geographical pattern in response types: billabongs on the Upper Murray and smaller tributaries show persistence of submerged plant communities over this period; billabongs from the middle Murray show almost universal loss of macrophytes; while billabongs from the Lower Murray show mixture of macrophyte loss, persistence of macrophytes and an unstable condition where there is no evidence of submerged macrophytes persisting for long periods. It is unclear whether this pattern reflects spatial variation in stressor intensity or underlying variation in the resilience of individual billabongs due, for example, to morphology, hydrology or location with respect to the main channel. This study explores the relationships between the degree of change in billabong ecosystems associated with European occupation and a range of morphological and landscape measures in an effort to determine the critical factors controlling resilience to the effects of land use and hydrological change.