Riverine ecosystem biodiversity is largely maintained by ecogeomorphic processes including vegetation renewal via uprooting and recovery times to flow disturbances. Plant roots thus heavily contribute to engineering resilience to perturbation of such ecosystems. We show that vegetation uprooting by flow occurs as a fatigue-like mechanism, which statistically requires a given exposure time to imposed riverbed flow erosion rates before the plant collapses. We formulate a physically based stochastic model for the actual plant rooting depth and the time-to-uprooting, which allows us to define plant resilience to uprooting for generic time-dependent flow erosion dynamics. This theory shows that plant resilience to uprooting depends on the time-to-uprooting and that root mechanical anchoring acts as a process memory stored within the plant–soil system. The model is validated against measured data of time-to-uprooting of Avena sativa seedlings with various root lengths under different flow conditions. This allows for assessing the natural variance of the uprooting-by-flow process and to compute the prediction entropy, which quantifies the relative importance of the deterministic and the random components affecting the process.