Nanotechnology is developing rapidly and, in the future, it is expected that increasingly more products will contain some sort of nanomaterial. However, to date, little is known about the occurrence, fate and toxicity of nanoparticles. The limitations in our knowledge are partly due to the lack of methodology for the detection and characterisation of engineered nanoparticles in complex matrices, i.e. water, soil or food. This review provides an overview of the characteristics of nanoparticles that could affect their behaviour and toxicity, as well as techniques available for their determination. Important properties include size, shape, surface properties, aggregation state, solubility, structure and chemical composition. Methods have been developed for natural or engineered nanomaterials in simple matrices, which could be optimized to provide the necessary information, including microscopy, chromatography, spectroscopy, centrifugation, as well as filtration and related techniques. A combination of these is often required. A number of challenges will arise when analysing environmental and food materials, including extraction challenges, the presence of analytical artifacts caused by sample preparation, problems of distinction between natural and engineered nanoparticles and lack of reference materials. Future work should focus on addressing these challenges.