Microplastics released into freshwaters from anthropogenic sources settle in the sediments, where they may pose an environmental threat to benthic organisms. However, few studies have considered the ecotoxicological hazard of microplastic particles for nematodes, one of the most abundant taxa of the benthic meiofauna. This study investigated the toxic effects of polystyrene (PS) beads (0.1-10.0 μm) and the underlying mechanisms thereof on the reproduction of the nematode Caenorhabditis elegans. The observed effect of the PS beads on the nematodes correlated well with the total surface area of the beads per volume, with a 50% inhibition of reproduction at 55.4 ± 12.9 cm2/mL, independent of the bead size. The adverse effects were not explained by styrene monomers leaching from the beads because chemical activities of styrene in PS suspensions were well below the toxic levels. However, the observed effects could be related to the bead material because the same-sized silica (SiO2) beads had considerably less impact, probably due to their higher specific density. PS and SiO2 beads affected the food availability of C. elegans, with greater effects by the PS beads. Our results demonstrate the importance of including indirect food web effects in studies of the ecological risks posed by microplastics.