Floodplain trees are responsive to disturbance and can be representative of broader patterns in ecosystem alteration. Over the past 20-30 years, continual declines in native riparian tree biomass has occurred in Australia’s highly regulated Murray-Darling Basin, although dominant spatial-temporal causes remain unclear. Adaptive cycles (panarchy) describe the dynamic responses of ecosystems to disturbance as a cyclic process. Here, we explore the utility of panarchy to interpret a ~30 year remotely sensed Normalized Difference Vegetation Index (NDVI) time series for two floodplain trees; Eucalyptus camaldulensis and E. largiflorens. We compared flood history in two large floodplain complexes in the MDB (Darling River - E. largiflorens; Yanga National Park – E. camaldulensis). The Yanga complex is highly managed, with environmental water regularly used to support tree health; in contrast, Darling River trees are more reliant on unregulated flows. We compare trajectories of change and potential thresholds which might indicate potential ‘flips’ of our case study ecosystems to less productive states. For the Darling River complex, trajectories were compared for trees inundated for 1:8 and >1:30 years, while three flood classes at Yanga of 1:2, 1:5 and 1:10 were compared. As flood frequency decreased, trajectories of NDVI progressed from a pattern of ~5-year cyclical positive/negative trajectories to long-term NDVI declines for the >1:30 and 1:10 flood classes. Long-term declines in the trajectory of the 1:8 flood class coincided with substantially reduced river flows in the Darling River from 1990 onwards. Additionally, substantial flooding in 2016 was not sufficient to reverse that decline. Our work has important implications for the management of water dependent ecosystems and we demonstrate the utility of panarchy for the exploration of resilience in floodplain ecosystems.