Large-scale Japanese lakes support many fish species and abundant fisheries resources. However, long-term changes in the fish fauna of such lakes have not been fully investigated, despite recent significant anthropogenic impacts on associated ecosystems. Accordingly, the extensive native and non-native fish fauna of Lake Kitaura, a typical large inland-sea lake (36 km2) in eastern Japan, was investigated based on specimens collected by the staff of Itako Hydrobiological Station, Ibaraki University from 1977 to 1997, plus data from previous studies conducted since the 1950s. In total, 83 species in 35 families have been recorded from the lake from the 1950s to the present decade. The analyses of long-term changes in fish species data since the 1960s demonstrated a sharp decrease in marine, estuarine and diadromous species due to an estuarine barrage (Hitachi River floodgate) established in 1973, the disappearance of nine red-list species (e.g., threatened and near threatened species) following various artificial environmental changes from the 1960s to 1980s, and an increase in introduced exotic and Japanese species after the 1980s.