Understanding and subsequently controlling non-specific interactions between engineered nanomaterials and biological environment have become increasingly important for further developing and advancing nanotechnology for biomedical applications. Such non-specific interactions, also known as the biofouling effect, mainly associate with the adsorption of biomolecules (such as proteins, DNAs, RNAs, and peptides) onto the surface of nanomaterials and the adhesion or uptake of nanomaterials by various cells. By altering the surface properties of nanomaterials the biofouling effect can lead to in situ changes of physicochemical properties, pharmacokinetics, functions, and toxicity of nanomaterials. This review provides discussions on the current understanding of the biofouling effect, the factors that affect the non-specific interactions associated with biofouling, and the impact of the biofouling effect on the performances and functions of nanomaterials. An overview of the development and applications of various anti-biofouling coating materials to preserve and improve the properties and functions of engineered nanomaterials for intended biomedical applications is also provided.