Climate change is expected to make many regions of the world much drier over coming decades1,2. More intense drought would transform rivers3 with potentially severe but largely unknown consequences at higher (multispecies) levels of organization4. Here we show experimentally how the intensification of drought may alter the underlying structure and functioning (biomass flux dynamics) of freshwater food webs - networks of species and their interactions5. Drought triggered substantial losses of species and links, especially among predators, leading to the partial collapse of the food webs. Total resource-consumer biomass flux was also strongly suppressed by disturbance, yet several network-level properties (such as connectance and interaction diversity) were conserved, driven by consumer resource fidelity and a substantial reconfiguration of fluxes within the webs as production shifted down the size spectrum from large to small species. Our research demonstrates that drier climates could have far-reaching impacts on the functioning of freshwater ecosystems.