Several observations and model calculations suggest that chemically mediated interactions can structure planktonic food webs. However, only recently have improvements in chemical methods, coupled with ecological assays, led to the characterization of chemical cues that affect the behaviour and/or physiology of planktonic organisms. We are currently beginning to elucidate if or how chemical signals can directly affect the interactions between species and even shape complex community structures in aquatic systems. Here, we highlight recent research on the nature and action of chemical signals in the pelagic marine and freshwater environments, with an emphasis on kairomones and defence metabolites.