Upper reaches of temperate streams and oligotrophic lakes depend trophically on the organic matter coming from the surrounding watershed. These aquatic ecosystems accumulate particulate and dissolved organic matter, and chemical compounds liberated from decomposing leaves or from the leachates of leaf litter. These materials supply a wide range of chemical compounds, which may serve as food, but also cause ecotoxicological effects on aquatic organisms. However, this ecotoxicological risk has been amply ignored, especially for freshwater invertebrates. The aims of our study are: (1) to assess the direct toxicity of aqueous extracts of leaf litter from two native (Populus alba, Fraxinus angustifolia) and two tree species exotic to Europe (Robinia pseudoacacia, Ailanthus altissima) on a pelagic and a benthic species of model aquatic invertebrates: Daphnia magna (Cladocera) and Potamopyrgus antipodarum (Mollusca) and (2) to estimate the ecotoxicological risk of the leaf litter extracts to lacustrine ecosystems using different simulated scenarios of shallow lakes. For both invertebrate species, we assessed the effective concentration of leaf extract causing an effect on 50% of the population (EC50) by means of laboratory bioassays. Our results show that the extracts of leaf litter from all the tested trees have a potential ecotoxicological risk in some scenarios, which is independent from the geographic origin of the tree species.