The unique chemical and physical properties of engineered nanomaterials that make them attractive for numerous applications also contribute to their unexpected behaviour in the environment and biological systems. The potential environmental risks, including their impact on aquatic organisms, have been a central argument for regulating the growth of the nanotechnology sector. Here we show in a simplified food web that carboxylated and biotinylated quantum dots can be transferred to higher trophic organisms (rotifers) through dietary uptake of ciliated protozoans. Quantum dot accumulation from the surrounding environment (bioconcentration) was limited in the ciliates and no quantum dot enrichment (biomagnification) was observed in the rotifers. Our findings indicate that dietary uptake of nanomaterials should be considered for higher trophic aquatic organisms. However, limited bioconcentration and lack of biomagnification may impede the detection of nanomaterials in invertebrate species.