In the last decades, the aquatic vegetation of the river Rhine has declined. In order to rehabilitate the vegetation in the river it is vital to gain insights in the environmental factors that affect the occurrence and establishment of aquatic macrophytes. Especially navigation is expected to negatively influence the environmental conditions through generating water displacements that changes flow velocities in the littoral zones. The aim of this study was to assess the effect of navigation on occurrence of aquatic macrophytes species in the river Rhine by 1) deriving a comprehensive overview of their sensitivities to flow velocity with the use of species sensitivity distributions (SSDs), and 2) calculating the potentially not occurring fraction (PNOF) of their species pool based on measurements of flow velocities during ship passages at various types of littoral zones. Maximum flow velocity sensitivity ranged from 43 to 120 cm sö1. Field measured flow velocities fluctuated mostly between 0 and 10 cm sö1. However, maximum measured flow velocities during ship passages ranged between 45 and 74 cm. sö1. This resulted in a PNOF value of almost 0.50, indicating that 50% of the plant species is potentially absent due to ship generated changes in flow velocities. As shipping intensity is expected to increase in the future the likelihood of flow velocities limiting macrophytes is expected to increase. This highlights the need of constructing connected backwaters, side channels and shore channels behind longitudinal training dams as they decrease the influence of navigation on flow velocity.