Aquatic ecosystems constitute essential models to understand the role of biodiversity and that of biotic and abiotic interactions on both community structure and ecosystem functioning. The last decade was marked by important breakthroughs: 1) The role of organism heterogeneity within food webs is better defined and the linear approaches in which the organisms are aggregated within distinct trophic levels are progressively left aside. Food-web study on the basis of functional groups made it possible to integrate the role of body size and omnivory within communities. Including the organisms of the microbial loop in food webs has increased our understanding of organic matter recycling and nutrient transfer to higher trophic levels; 2) The topological analysis of the food webs allows to consider trophic networks in their complexity and to establish their architectural characteristics. Attempts are made to counterbalance interspecific trophic links by an occurrence probability or by an interaction strength, in particular by taking into account the functional features of species, prey/ predator relative sizes and allometric rules; 3) Food-web studies in homogeneous biotopes, such as the pelagic zones of lakes, allowed a significant progress in the understanding of the top-down vs. bottom-up control of communities. However, taking into account the vertical, horizontal or temporal heterogeneity of the ecosystems not only increased the realism of food-web structures, but made it possible to consider the temporal dynamics of the couplings between various systems (pelagic zone-littoral zone, water-sediment, catchment area-aquatic ecosystem, upstream-downstream, etc.); 4) The coupling between biogeochemical cycles and trophic interactions is progressively integrated. This is favoured by the development of ecological stoichiometry, which studies the links between the chemical composition of organisms (in carbon, nitrogen or phosphorus) and biotic interactions (primary production, herbivory, decomposition, etc.); 5) There is a significant increase in the comparative approaches, the conceptual exchanges and the effective couplings between the ecology of terrestrial and aquatic systems; 6) New concepts and tools allow an increasingly sharp consideration of heterogeneity and complexity from the molecular level up to the ecosystem. The importance of non-trophic interactions, for example the role of chemicalinformation mechanisms (allelopathy, etc.), is more and more studied. The monitoring or the addition of tracers, such as stable isotopes, made it possible to detect new patterns and to integrate many processes, from the molecular level to the ecosystem scale (analysis of the trophic positions of species, analysis of the allochtonous contributions, etc.). The objective is now to integrate this multidimensional complexity in order to reach a better prediction capacity of limnology as a discipline for human societies.