Natural aquatic colloids are materials with one dimension between 1 nm and 1 mu m. More informally defined, nanoparticles are materials with at least one dimension less than 100 nm. Both colloids and nanoparticles have significant effects on pollutant, nutrient, and pathogen chemistry, transport and bioavailability, and may themselves be bioavailable. Techniques for their fractionation, characterization and analysis have improved greatly in recent years. Although knowledge of their structure and environmental impact has also increased, it has not done so to the same degree and thus the field awaits the substantial application of new methodologies. This paper reviews the current state of the art in this area and also discusses likely future developments.