Lake ecosystems are exposed to a range of anthropogenic pressures, particularly eutrophication, and in some cases also stocking and/or overfishing of top-predator fish species, all factors that have implications for the food web structure and which could lead to dominance of nuisance cyanobacteria. Restoration of degraded lakes demands insight into the relative role of top-down for bottom-up regulating forces. While knowledge about these forces in temperate lakes is extensive, comparatively little is known of their role in subtropical lakes where the importance of herbivorous and benthic feeding fish is higher. Here, we analyzed a long-term monitoring data set on subtropical, shallow Lake Taihu, China, and applied random forests regression to examine how phytoplankton was related to environmental variables and biotic assemblages. Our results indicate that the biomass and density of phytoplankton increased with increasing biomass of benthivorous and zooplanktivorous fish and decreased with increases in ammonium concentrations, the nitrogen to phosphorus ratio, and zooplankton biomass, while the response to climate fluctuations and changes in the biomass of piscivores was weak. Effects of higher trophic levels explained as much of the variance in phytoplankton biomass as did nutrients and climatic factors. Moreover, the remarkably reduced ratio of zooplankton to phytoplankton biomass and the decline in cladoceran individual biomass emphasized the increasing importance of top-down control in regulating the phytoplankton following extensive stocking. Our findings offer insight into how fish management may be combined with catchment-level restoration measures to conserve and enhance water quality.