The industrial scale production and wide variety of applications of manufactured nanoparticles (NPs) and their possible release in considerable amounts into the natural aquatic environment have produced an increasing concern among the nanotechnology and environmental science community. In order to address this issue, it is important to understand NP chemistry, preparation, reactivity and possible mechanisms involved in their interaction with the naturally occurring aquatic components, particularly natural colloids and NPs present in the aquatic systems. In this review, an overview of the chemistry of both manufactured and natural aquatic NPs is outlined. This review discusses the physico-chemical aspects of both type of NPs as an essential point to assess possible routes involved in manufactured NP fate in the natural aquatic environment and their toxicity. Key advances related to the characterisation of the manufactured NPs and natural colloids.