Sediment deposition and bank accretion are promoted by the establishment and growth of pioneer plant species, a direct consequence of plant survival during flood events. Similarly, the uprooting of riparian vegetation on river bars during floods can subsequently alter hydraulics, sediment dynamics, and bar evolution. In this work, we focus on the removal of flexible seedlings due to both hydraulic forces and bed erosion, specifically examining failure mechanisms associated with root pull-out. We provide a conceptual model and a new physical equation for predicting the flow and bed erosion conditions that promote the uprooting of plants. The model was validated by means of flume experiments employing two species of vegetation (i.e., common oats and a willow native to Europe). Furthermore, the Ombrone Pistoiese River (Tuscany, IT) was used as a case study to validate the physical model with respect to observed vegetation removal during a flood event. The results illustrate the capability of our model to predict conditions for vegetation removal and suggest that sediment transport is a necessary ingredient even for very young seedlings.