Vessel-induced waves affect the morphology and ecology of banks and shorelines around the world. In rivers used as waterways, ship passages contribute to the erosion of unprotected banks, but their short-and long-term impacts remain unclear. This work investigates the effects of navigation on bank erosion along a reach of the regulated Meuse River with recently renaturalized banks. We apply UAV-SfM photogrammetry, RTK-GPS, acoustic Doppler velocimetry, aerial and terrestrial photography, soil tests, and multibeam echosounding to analyze the progression of bank retreat after riprap removal. After having analyzed the effects of ship-generated waves and currents, floods, and vegetation dynamics, a process-based model is proposed to estimate the long-term bank retreat. The results show that a terrace evolves in length and depth across the bank according to local lithology, which we clustered in three types. Floods contribute to upper-bank erosion-inducing mass failures, while near-bank flow appears increasingly ineffective to remove the failed material due to terrace elongation. Vegetation growth at the upper-bank toe reduces bank failure and delays erosion, but its permanence is limited by terrace stability and efficiency to dissipate waves. The results also indicate that long-term bank retreat is controlled by deep primary waves acting like bores over the terrace. Understanding the underlying drivers of bank evolution can support process-based management to optimize the benefits of structural and functional diversity in navigable rivers. Plain Language Summary Ship waves can be an important cause of bank erosion and ecological disturbance in rivers used as waterways. Despite present needs to improve riverine habitats, our understanding of ship-generated erosion is still poor. This is the first systematic and thorough investigation of bank erosion processes driven by ship waves. We focus on a river reach with recently renaturalized banks presenting diverse erosion rates to study the mechanisms and factors that determine bank retreat. The results show that banks retreat forming a terrace with length and depth that mainly depend on soil composition. Floods are responsible for bank collapse, but the near-bank flow gradually reduces as the terrace extends. As a result, floods become eventually unable to remove the failed material and produce further bank retreat. Plants and trees growing at the bank toe delay erosion, but their survival depends on the terrace evolution. Based on the analysis of field data, we developed a model to predict the final extent of bank retreat. Our results indicate that primary ship waves, acting like bores, determine the ultimate terrace shape. Understanding how banks erode due to navigation allows practitioners and managers to improve the ecological conditions of riparian habitats.