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Synergies between large-scale environmental changes, such as climate change1 and increased humic content (brownification)2, will have a considerable impact on future aquatic ecosystems. On the basis of modelling, monitoring and experimental data, we demonstrate that community responses to global change are determined by food-chain length and that the top trophic level, and every second level below, will benefit from climate change, whereas the levels in between will suffer. Hence, phytoplankton, and thereby algal blooms, will benefit from climate change in three-, but not in two-trophic-level systems. Moreover, we show that both phytoplankton (resource) and zooplankton (consumer) advance their spring peak abundances similarly in response to a 3 °C temperature increase; that is, there is no support for a consumer/resource mismatch in a future climate scenario. However, in contrast to other taxa, cyanobacteria—known as toxin-producing nuisance phytoplankton3—benefit from a higher temperature and humic content irrespective of the food-chain composition. Our results are mirrored in natural ecosystems. By mechanistically merging present food-chain theory with large-scale environmental and climate changes, we provide a powerful framework for predicting and understanding future aquatic ecosystems and their provision of ecosystem services and water resources.

Climate change is altering temperatures and precipitation patterns all over the world. In Patagonia, Argentina, predicted increase in precipitation together with rapidly melting glaciers increase the surface runoff, and thereby the transport of suspended solids to recipient lakes. Suspended solids affect the visual conditions in the water which in turn restricts visual foraging. The native fish Aplochiton zebra Jenyns, and its filter-feeding cladoceran prey, Daphnia commutata Ekman, were subjected to foraging experiments at three turbidity levels. A. zebra foraging rate was substantially reduced at naturally occurring turbidity levels and the filtering rate of D. commutata was reduced at the highest turbidity level. This indicates that Daphnia may be partly released from predation from A. zebra at the same time as it can maintain relatively high feeding rates as turbidity increases. Lower foraging rates at the same time as the metabolic demand increases, through increased temperatures, may result in larger effects on A. zebra than could be expected from increases in turbidity or temperature alone. Turbidity may, as an indirect effect of climate change, decrease planktivore foraging rates and thereby alter the interaction strength between trophic levels.