Increasing activity in the growing field of nanotechnology will likely contaminate aquatic ecosystems and perhaps adversely affect living organisms. The present review addresses the potential impacts of nanotechnology on aquatic ecosystems. The degree of the persistence of nanomaterials (NMs) in aquatic compartments is largely unknown, but preliminary experiments on selected NMs showed that they tend to partition, preferably first to the sediment, then to the water column. Cadmium telluride, fullerene (C60) and strontium ferrite were the most soluble substances. The toxicity of these NMs was investigated using a multitrophic test battery, which revealed that bacteria, invertebrates (Hydra) and trout hepatocytes sensitively responded to some of them. Moreover, NMs were able to increase the toxicity of both the sediment and elutriate of a certified reference sediment. The toxicity of NMs is likely to arise from the four fundamental properties associated with colloids: 1) the leaching of small-molecular-weight molecules or ions, 2) the size or shape of the NMs 3) the surface properties (reactivity),  and 4) the vectorization effect or transport of contaminants. New biomarkers, some of them derived from toxicogenomics, will be proposed to measure the effects associated with the particle size and surface properties of these colloids. Special attention is given to assessing their cumulative effects on aquatic ecosystems.