In recent years, the implication of genomics into ecotoxicological studies has been studied closely to allow a better understanding of organism’s responses to environmental contaminants including engineering nanomaterials (ENMs). ENMs are increasingly produced for various applications including cosmetics, electronics, sports equipment, biomedicine and agriculture. Because of their small size, ENMs possess chemical or physical characteristics improved compared to the corresponding macro-sized material. As their application expend, the release of manufactured ENMs into the environment is likely to increase and concern over impacts for the aquatic ecosystem is growing. Several studies reported deleterious effect of ENMs to aquatic organisms, but there is little information about the molecular mechanisms of toxicity. The development of ecotoxicogenomic approaches will improve the characterization of cellular and molecular modes of action of ENMs to aquatic organisms and allow a better prediction of contaminants toxicity. This paper presents an overview of transciptomic/proteomic studies in freshwater and marine organisms exposed to ENMs. Overall, induction of gene expression in relations to defense mechanisms, immune responses, growth and reproduction were measured after ENMs exposures of organisms, but with different patterns depending on exposure duration and concentrations used. In addition, some studies reported a positive correlation between gene expression and cellular modifications, but not at the individual level.