Short-term data on ecological condition have been used to underpin the case for restoring the balance of water between production and environment in the Murray–Darling Basin, Australia, even though trends of ecological time series provide a more informative picture. We assessed trends of 128 data series (mean 22 years, spanning 1919-2012) on floodplain vegetation, aquatic macroinvertebrates, reptiles and amphibians, fishes and waterbirds. Of 114 series (excluding invasive species and initial-final studies), 55 (48%) showed monotonic (n = 49) or step-change (n = 6) declines, but 59 (52%) were stable (n = 52) or showed a monotonic increase (n = 7). There was no significant relationship between type of trend and ecological component, response variable, duration, number of data-points or years of drought. Declines pre-dated the Millennium Drought (1997-2010) and increased irrigation diversions from the 1950s (though only 15 series commenced pre-1950) and are likely due to differential effects of multiple long-term stressors. Improvements in response of 22/40 series after the Millennium Drought support our finding that the most common pattern is of stability with fluctuations between wet and dry conditions, indicating that resilience of flow-dependent ecosystems of the Basin may be higher than has been anticipated.