Engineered nanoparticles (ENPs) are increasingly being incorporated into commercial products. A better understanding is required of their environmental impacts in aquatic ecosystems.This review deals with the ecotoxicity effects of silver and gold ENPs (AgNPs and AuNPs) in aquatic organisms, and considers the means by which these ENPs enter aquatic environments, their aggregation status and their toxicity. Since ENPs are transported horizontally and vertically in the water column, we discuss certain factors (e.g., salinity and the presence of natural organic materials), as they cause variations in the degree of aggregation, size range and ENP toxicity. We pay special attention to oxidative stress induced in organisms by ENPs.We describe some of the main analytical methods used to determine reactive oxygen species, antioxidant enzyme activity, DNA damage, protein modifications, lipid peroxidation and relevant metabolic activities. We offer an overview of the mechanisms of action of AgNPs and AuNPs and the ways that relevant environmental factors can affect their speciation, agglomeration or aggregation, and ultimately their bio-availability to aquatic organisms.Finally, we discuss similarities and differences in the adverse effects of ENPs in freshwater and salt-water systems.