The structure of aquatic ecosystems is determined by complex interactions among individual organisms at different trophic levels. Although our basic understanding of how top-down and bottom-up processes interact to determine food-web dynamics has advanced, we still lack insights into how complex interactions and feedbacks affect the dynamics and structure of food webs. It is now becoming increasingly clear that, in addition to energy transfer from one trophic level to the other, there is exchange of information between these levels facilitated by the release of infochemicals by the organisms. There is evidence from recent studies that the exchange of chemical information in freshwater ecosystems is likely to play a decisive role in shaping structure and functioning of these systems. Chemical communication among freshwater organisms mediates many aspects of both predation and interspecific competition, which play key roles in determining community structure and ecosystem functioning. For example, consumer-induced defences in phytoplankton and zooplankton include modifications in the characteristics relating to life history, behaviour, morphology and biochemistry. These inducible defences affect trophic interactions by altering predator feeding rates through changes in attack rate or handling time, or both. Also host-specific fungal parasitism in phytoplankton is probably controlled by infochemicals. The motile fungi recognise their host by host-secreted compounds. Until now models describing the functioning of ecosystems mainly considered flows of biomass and energy. Integration of new knowledge about the role of chemical communication in these models may be one of the aims of ecological informatics. In this chapter I discuss how infochemicals may affect the dynamics and structure of planktonic food webs.