Lake Biwa has experienced eutrophication from late 1960s to mid 1980s. Yet, little is known how eutrophication affected the dynamics of Lake Biwa’s dominant zooplankter, the calanoid copepod Eodiaptomus japonicus. We used long-term series data (1963-1990) on density, clutch size and body size to investigated E. japonicus responses to eutrophication at different temporal scales and explore the potential mechanisms associate with the responses. A well-pronounced decline in E. japonicus abundance occurred during nutrient loading rise (1966 – 1974), coincident with a decrease in clutch size, and smaller adult females due to increasing predator pressure. The decrease in E. japonicus abundance then slackened and the seasonal pattern of density and clutch size shifted from an unimodal to a bimodal one. This change, occurring during nutrient loading waning, was most likely induced by changes in the phytoplankton community, combined with reduced predation pressure. After the stabilization of nutrient loading in 1985, E. japonicus abundance increased and exhibited again a unimodal seasonal pattern. These findings contribute to the debate about the use of E. japonicus as indicator of environmental changes in Lake Biwa.