The sediment samples of zooplankton subfossil at different depths were collected from a large shallow lake Wuliangsuhai Lake, China, in order to reconstruct lake past changes. The lake began to switch to eutrophication gradually in the middle 1980s, creating a sediment discontinuity layer (about 32.5 cm depth) that can be visually used to separate sediments derived from plankton and macrophyte. Inferences about the timing and trajectory of eutrophication were made using sediment zooplankton subfossil reconstruction. The changes in composition of the zooplankton fragments were rather gradual up the core, whereas the total numbers of fragments show the most marked changes from 32.5 cm to present. Changes in the composition of zooplankton fragments (in 32.5 cm depth) show a gradual shift from a “pelagic community” dominated by B. longirostris, reflecting clearwater conditions with high predation pressure, to a more “benthic” community, dominated by plant associated Chydorids. The results suggest that it is possible to reconstruct past eutrophication trends of the lake by using zooplankton subfossil, and that anthropogenic pollutant loading is the key factor in the eutrophication of Lake Wuliangsuhai.