The impact of eutrophication on aquatic ecosystems remains an important topic in aquatic ecology; however, recent successes in water quality restoration in highly eutrophicated water bodies present new research potential regarding re-oligotrophication. Successfully reducing nutrient loading from sewage treatment through restoration activities, induces large changes in phytoplankton composition and biomass, particularly replacement of cyanobacterial dominance. In Lake Suwa, a shallow eutrophic lake in central Japan, recovery has occurred due to water quality restoration efforts since the 1970s. The improvement of lake trophic state from hypertrophic to mesotrophic is accompanied by various changes, such as rapid decreases in biomass of phytoplankton, benthic invertebrates and planktivorous pond smelt, and increases in biomass of aquatic vegetation, mainly floating leaved plants. During re-oligotrophication, zooplankton are important because they are major secondary producers in lake ecosystems. In Lake Suwa, the Research and Education Center for Inland Water Environment, Shinshu University has collected bi-weekly zooplankton samples and analyzed species composition since 1996, when the lake was in a hypertrophic state with serious Microcystis blooms. Lake Suwa is one representative lake for re-oligotrophication in a shallow eutrophic system, and our zooplankton dataset can be used to understand the changes in ecosystem structure and function.