Abstract: We compiled and analyzed long-term data, including chemical, physical and phytoplankton community data, for the Lake Biwa ecosystem from 1962 to 2003. Analyses on environmental data indicate that Lake Biwa had experienced intensified eutrophication (according to total phosphorus concentration) in the late 1960s and returned to a less eutrophic status around 1985, and then exhibited rapid warming and thus increased water column stability since 1990. Total phytoplankton cell volume largely followed the trend of total phosphorus concentration, albeit short-term fluctuations existed. However, phytoplankton community shifted dramatically in response to those changes of environmental states. These shifts were cause by changes in trophic status driven by phosphorus loadings and physical properties in the water column driven by warming. Moreover, most phytoplankton species did not show a strong linear correlation with environmental variables, suggesting nonlinear transitions among different states.