Many palaeoecological records from the Murray-Darling Basin show evidence of abrupt submerged plant loss associated with the beginning of European occupation. However, poor chronological control of sediment records has made it difficult to determine the driver(s) of these changes and whether the changes are the result of non-linear, threshold responses or more simple responses to an abrupt introduction of an intense stressor. This study explores these uncertainties by first establishing expected spatial and temporal patterns in the onset and intensity of non-indigenous anthropogenic stressors likely to have impacted billabongs. Next, these ‘driver surfaces’ are compared with observed changes in billabong palaeo records to determine which drivers best explain the observed ecosystem responses. Finally, the temporal patterns of change are modelled to determine if responses are best characterised as non-linear step changes, reflecting threshold responses, linear, though abrupt, changes reflecting abrupt stressor onset or gradual linear responses.