The increasing use of engineered nanomaterials (ENMs) will inevitably result in their release into natural environment and thereby lead to the exposure of living organisms. Hence, a new concern has arisen for the risk assessment of these emerging contaminants in the natural environment, especially in aquatic systems as an important sink and exposure source. Reducing the release of nanomaterials into water could contribute significantly to reducing exposure. Thus it is vital to consider how to manage wastewater containing such ultrafine nano-objects. This review provides an overview of technologies (classical and innovative) for nanomaterials separation/removal, which are discussed in terms of their advantages and disadvantages, as well as parameters affecting removal efficiency. To investigate the occurrence and fate of ENMs in the aquatic environment, the development of appropriate approaches for their separation prior to analysis is needed urgently. Finally, a brief summary of techniques for sample preparation and fractionation of ENMs in the natural aquatic environment is presented.