It has been shown that microplastics (MPs) interfere with critical biological processes (including development, growth and fitness); however, there is no information about the impact of MPs on plant productivity and community structure in freshwater ecosystems. Here, we investigated the effects of two sizes (MIC: 20–300 μm, MAC: 2–3 mm) and three concentrations (0.03 %, 0.3 %, and 0.6 %) of low-density polyethylene MPs on submerged plant communities. The results showed that plant responses to MPs were species specific, which can affect plant community structure. For canopy-forming species (Hydrilla verticillata), total biomass increased by 4 %–46 % and relative abundance increased by 23 %–34 % under MP exposure, while rosette-forming species (Vallisneria natans) decreased by 44 %–67 % in total biomass and relative abundance decreased by 54 %–71 %. Myriophyllum spicatum growth was largely unaffected by MPs. Community diversity was negatively correlated with MAC treatments, and the community root to shoot ratio decreased by 40 %, while community productivity increased by 41 % at a 0.6 % MAC concentration. Although MPs did not change the microbial community composition, alpha diversity was reduced at the 0.6 % concentration. It is worth noting that 0.6 % is a higher concentration than most field sediment investigations. During the experiment, the activity of functional enzymes related to carbon and nitrogen increased under most MP treatments. Structural equation modelling showed that MIC changed the community structure mainly by driving sediment enzyme activity, while MAC changed the community structure mainly by driving plant growth. The results implied that MPs may affect sediment enzymatic activities, microbial alpha diversity and aquatic plant growth, potentially altering the diversity and stability of aquatic ecosystems.