Compared to its terrestrial counterpart, chemical ecology has only recently been applied to aquatic organisms. The delay in this area is mainly due to the difficulty in accessing marine or freshwater habitats. Indeed, the discovery of the biological diversity inhabiting our oceans associated with their chemical diversity only started in the late 1950s with the development of SCUBA diving. Just as the terrestrial plants, the first studied macroorganisms present in coastal waters were found to host an unexpected diversity of unique metabolites. As life first appeared in our oceans, the chemical structures of aquatic metabolites have been finely tuned to exert their ecological role along their evolutionary history. The highly polar and protic properties of the water molecule acting as the surrounding medium of aquatic organisms induced original chemical architectures for the aquatic chemical cues involved into contact and distance interactions. Where some level of similarities was found between aquatic and terrestrial metabolic pathways, some are specific to aquatic environments leading for instance to a higher number of nitrogen and halogens. In more than 70 years, some progress has been made in the understanding of the chemically mediated interactions in the aquatic environment, but this field is still largely understudied. Some peculiarities are identified between freshwater and marine chemical mediators mainly because of the difference in salinity. More recently, some pioneering works were also undertaken to unravel the ecological roles of metabolites produced by aquatic microorganisms. This special issue highlights recent work in different aspects of aquatic chemical ecology covering a broad range of organisms from freshwater to marine environments applied to micro- and macroorganisms. Investigations are also directed towards the effects of the changes of environmental parameters on chemically mediated interactions between aquatic species.