The extent to which ecosystems are regulated by top-down relative to bottom-up control has been a dominant paradigm in ecology for many decades. For lakes, it has been shown that predation by fish is an important determinant of variation in zooplankton and phytoplankton community characteristics. Effects of fish are expected to not only be a function of total fish biomass, but also of functional composition of the fish community. Previous research on the importance of trophic cascades in lakes has largely focused on the role of zooplanktivorous and piscivorous fish. We conducted a large-scale multiple-lake fish community manipulation experiment to test for the effect of differences in fish functional community composition on the trophic structure of lakes. We examine the effect of top-down and bottom-up factors on phytoplankton and zooplankton biomass as well as on their community composition. We put our data in a broader perspective by comparing our results to data of a survey that also included ponds with low fish densities as well as ponds with very high densities of fish. Our results indicate that the overall food web structure under relative high fish densities is primarily structured by bottom-up factors, whereas community characteristics seem to be primarily regulated by top-down factors. Our results suggest a subtle interplay between bottom-up and top-down factors, in which bottom-up factors dominate in determining quantities while top-down effects are important in determining identities of the communities.