Plastic debris of all sizes has been detected in marine, terrestrial and freshwater habitats. Effects of plastic debris on macrophytes have hardly been studied, despite their importance in aquatic ecosystems. We provide the first experimental study exploring nano- and microplastic effects on the growth of sediment-rooted macrophytes. Myriophyllum spicatum and Elodea sp. were exposed to sediments amended with six doses of polystyrene (PS) nanoplastic (50–190 nm, up to 3% sediment dry weight) and PS microplastic (20–500 μm, up to 10% dry weight) under laboratory conditions. Both macrophyte species were tested for changes in root and shoot dry weight (DW), relative growth rate (RGR), shoot to root ratio (S:R), main shoot length and side shoot length. Microplastics did not produce consistent dose-effect relationships on the endpoints tested, except that main shoot length was reduced for M. spicatum with increasing microplastic concentration. Nanoplastic significantly reduced S:R for both macrophytes as a result of increased root biomass compared to shoot biomass. Nanoplastic also caused a decrease in M. spicatum main shoot length; however, shoot biomass was not affected. Elodea sp. side shoot length, root and shoot biomass and RGR were positively correlated to the nanoplastic concentration. All effects occurred at higher than environmentally realistic concentrations, suggesting no immediate implications for ecological risks. Our study did not aim for the elucidation of the exact mechanistic processes that cause the effects, however, particle size seems to play an important factor.