In our paper 'Effect of shipping induced changes in flow velocity on aquatic macrophytes in intensively navigated rivers' (10.1016/j.aquabot.2019.103145), we used literature data of flow velocity tolerances of macrophytes to construct species sensitivity distributions (SSDs). With these SSDs and field measurements of flow velocities during ship passages at various types of littoral zones, potentially not occuring fractions (PNOFs) were calculated. Maximum flow velocity sensitivity ranged from 43 to 120 cm s-1. 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. s-1. 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. In this repository, we provide the literature based tolerance data of macrophytes, the maximum flow velocity during ship passages and flow velocity measurements at four different locations along the river Rhine on six days in 2017.This dataset includes the following four data files:1. 'Data from literature for SSD', which includes all the data collected from literature concerning flow velocity tolerances of macrophytes occurring in the river Rhine.2. 'Field data_max_flow_velocity_passing_ships' is a dataset including all the passing ships included in the study. Information about their name, direction, distance from flow velocity sensors and the maximum flow velocity are also included.3. 'Flow_velocity_all_locations' includes all the flow velocity measurements at each location.4. 'Overview of literature data flow velocity tolerances macrophytes' gives an overview of the literature data concerning flow velocity tolerances of the macrophytes included in this study.