The specific properties of metal-based nanoparticles (NPs) have not only led to rapidly increasing applications in various industrial and commercial products, but also caused environmental concerns due to the inevitable release of NPs and their unpredictable biological/ecological impacts. This review discusses the environmental behavior of metal-based NPs with an in-depth analysis of the mechanisms and kinetics. The focus is on knowledge gaps in the interaction of NPs with aquatic organisms, which can influence the fate, transport and toxicity of NPs in the aquatic environment. Aggregation transforms NPs into micrometer-sized clusters in the aqueous environment, whereas dissolution also alters the size distribution and surface reactivity of metal-based NPs. A unique toxicity mechanism of metal-based NPs is related to the generation of reactive oxygen species (ROS) and the subsequent ROS-induced oxidative stress. Furthermore, aggregation, dissolution and ROS generation could influence each other and also be influenced by many factors, including the sizes, shapes and surface charge of NPs, as well as the pH, ionic strength, natural organic matter and experimental conditions. Bioaccumulation of NPs in single organism species, such as aquatic plants, zooplankton, fish and benthos, is summarized and compared. Moreover, the trophic transfer and/or biomagnification of metal-based NPs in an aquatic ecosystem are discussed. In addition, genetic effects could result from direct or indirect interactions between DNA and NPs. Finally, several challenges facing us are put forward in the review.