How will the current rate and spatial extent of environmental change affect the functioning of future ecosystems? Food webs are structurally diverse and are remarkably persistent despite multifaceted and spatially variable environmental change. Ecological theory posits that the structural complexity of food webs will help ecosystems weather environmental change, but few experiments have tested this idea. To truly understand how ecosystems and their constituent food webs will respond, we must explore, experimentally, how environmental change affects the structure of food webs, for example the number of species and the interactions among them, and, consequently, the the functioning of ecosystems, for example, the rates of biomass production, decomposition, and sequestration.Our proposed research focuses on the environmental changes associated with rising levels of dissolved organic carbon (DOC) in freshwater ecosystems, but also considers climate warming, eutrophication, and changes in biodiversity. As microbial communities closely regulate the decomposition of DOC, we propose to examine the effect of changes in the environment and in the architecture of food webs on the composition of microbial communities, including viruses and prokaryotes. In doing so, we can link the ecological structure and evolutionary dynamics of food webs to the biogeochemistry of ecosystems.We propose a series of experiments to test how environmental change affects the complex interactions between food web assemblages and ecosystem functioning. The experiments test predictions from three bodies of ecological theory, namely the theory of biodiversity and ecosystem functioning, the theory of evolving metacommunities, and the landscape theory of food-web structure. These theories provide a strong foundation for understanding interactions between environmental change, food-web architecture, and ecosystem functioning, but they fail to fully address the feedbacks between structural changes of food-webs at upper trophic levels (e.g. plankton and fish) and the biogeochemistry of ecosystems that is regulated by microbial communities. Our experiments bridge this gap, and will improve our ability to predict how entire ecosystems respond to environmental change.