This paper introduces a special issue on the ecotoxicology and environmental chemistry of nanoparticles (NPs), and nanomaterials (NMs), in the journal Ecotoxicology. There are many types of NMs and the scientific community is making observations on NP ecotoxicity to inform the wider debate about the risks and benefits of these materials. Natural NPs have existed in the environment since the beginning of Earth’s history, and natural sources can be found in volcanic dust, most natural waters, soils and sediments. Natural NPs are generated by a wide variety of geological and biological processes, and while there is evidence that some natural NPs can be toxic, organisms have also evolved in an environment containing natural NPs. There are concerns that natural nano-scale process could be influenced by the presence of pollution. Manufactured NPs show some complex colloid and aggregation chemistry, which is likely to be affected by particle shape, size, surface area and surface charge, as well as the adsorption properties of the material. Abiotic factors such as pH, ionic strength, water hardness and the presence of organic matter will alter aggregation chemistry; and are expected to influence toxicity. The physico-chemistry is essential to understanding of the fate and behaviour of NPs in the environment, as well as uptake and distribution within organisms, and the interactions of NPs with other pollutants. Data on biological effects show that NPs can be toxic to bacteria, algae, invertebrates and fish species, as well as mammals. However, much of the ecotoxicological data is limited to species used in regulatory testing and freshwater organism. Data on bacteria, terrestrial species, marine species and higher plants is particularly lacking. Detailed investigations of absorption, distribution, metabolism and excretion (ADME) remain to be performed on species from the major phyla, although there are some data on fish. The environmental risk assessment of NMs could be performed using the existing tiered approach and regulatory framework, but with modifications to methodology including chemical characterisation of the materials being used. There are many challenges ahead, and controversies (e.g., reference substances for ecotoxicology), but knowledge transfer from mammalian toxicology, colloid chemistry, as well as material and geological sciences, will enable ecotoxicology studies to move forward in this new multi-disciplinary field.