Question What is the role of wind in the dispersal of waterborne seeds in slow-flowing and stagnant water bodies at different temporal and spatial scales? (i) Is there a direct effect of wind on seed dispersal speed and distance? (ii) Are prevailing wind conditions reflected in the seed deposition patterns during a year? (iii) What are the long-term (multiple year) effects of prevailing wind conditions on the pattern and composition of shoreline seed banks? Location The Westbroekse Zodden (52˚10N; 5˚07E) and De Weerribben (52°46N; 5°55E) fen reserves in The Netherlands. Methods Real-time seed movement tracking experiments were conducted at different wind speeds. Additionally, we performed a seed trap experiment using artificial grass mats and carried out seed bank analyses using a seedling emergence test. Results Wind speed and direction strongly determined the dispersal process and the resulting deposition patterns of floating seeds in shallow lakes or ponds. Wind speed directly influenced dispersal speed and distance. Increasing wind speed increased dispersal speed but decreased dispersal distance. Over multiple seasons, more seeds were deposited at downwind shorelines than at upwind shorelines, showing that wind-driven hydrochory resulted in directional transport according to the prevailing wind direction. The species composition of deposited seeds was also affected, with proportionally more water-dispersed seeds being deposited at down-wind shorelines. These effects of wind speed and directionality will have consequences for the colonization of riparian zones in lentic systems and, therefore, also influence management and restoration. In the long term, local seed banks in riparian zones reflected the prevailing wind conditions poorly, showing that additional processes, such as differential germination and predation, also play important roles at longer time scales. Conclusions Wind plays an important role in the dispersal of waterborne seeds in lentic systems and (prevailing) wind speed and direction are reflected in seed dispersal trajectories and deposition patterns.