We investigated the impact of CeO2 nanoparticles (NPs) with different sizes, shapes and coatings on the function of a freshwater experimental ecosystem. We hypothesized that the different types of NPs would have different effects on the organisms involved in leaf litter decomposition and could differentially affect this process. Experiments were conducted in microcosm under environmentally relevant conditions with low CeO2 NP concentrations (1 mg L−1). Leaf litter decomposition, leaf-associated fungal biomass, bacterial community diversity and toxicity on Chironomus riparius larvae were studied. A decrease in teratogenicity (mouthpart deformities) in chironomid larvae was observed with citrate-coated spherical NPs, suggesting a hormesis effect. In contrast, exposure to non-coated, spherical NPs led to increased teratogenicity in chi- ronomids, changes in bacterial community diversity and decreased leaf litter decomposition. Large, non- coated plates induced changes in bacterial assemblages, whereas no effect on fungal biomass was ob- served. These results are discussed and several hypotheses are presented to explain the results. Leaf litter decomposition is a marker that is frequently used to assess freshwater ecosystems' health. Extending its use to nano-ecotoxicology enables the study of NP impact on the function of ecosystems. This study shows that leaf litter decomposition and mouthpart deformities in chironomid larvae are sensitive, congru- ent markers of the environmental impact of CeO2 NPs under these experimental conditions.