While theoretical food web studies highlight the importance of alternative energy pathways in shaping community response to bottom-up and top-down forcing, empirical insight on the relevance of the predicted patterns is largely lacking. In marine plankton food webs differences in food size spectra between ciliates and copepods lead to alternative energy pathways, one expanding from small phytoplankton over ciliates to copepods, the other from large edible phytoplankton directly to copepods. Correspondingly, predation pressure by copepods leads to an increase of small phytoplankton through top-down control of copepods on ciliates, but to a decrease of large phytoplankton through direct predation by copepods. Hence, food web theory predicts a shift from the dominance of large to small algae along an enrichment gradient. This prediction clearly deviates from the general assumption of a shift from small fast growing to larger slow-growing phytoplankton taxa with increasing nutrient availability. However, if copepods themselves are under top-down control by strong predation through planktivores such as fish or jellyfish, dominance of large algae is expected throughout the enrichment gradient. We tested these predictions by analyzing the phytoplankton composition from numerous marine lakes and lagoon sites located on the archipelago of Palau covering a wide range of nutrient levels, comparing sites lacking large numbers of higher trophic levels with sites harboring high densities of jellyfish. The observed patterns strongly support that higher trophic levels influence the phytoplankton size distribution along a nutrient enrichment gradient, highlighting the importance of alternate energy pathways in food webs for community responses.