Freshwater ecosystems along river floodplains host among the greatest biodiversity on Earth and are known to respond to anthropic pressure. For water impounded systems, resilience to changes in the natural flow regime is believed to be bi-directional. Whether such resilience prevents the system from returning to pristine conditions after the flow regime changes reverse is as yet unclear, though widely documented. In this work we show that temporal irreversibility of river floodplains to recover their status may be explained by the dynamics of riparian water-tolerant plant roots. Our model is a quantitative tool that will benefit scientists and practitioners in predicting the impact of changing flow regimes on long-term river floodplain dynamics.