Although ca. 67 indigenous fish species and subspecies inhabit the Lake Biwa water system, (Shiga Prefecture, central Japan), including many endangered taxa, studies on the continuity of fish habitat between Lake Biwa and inlet rivers are few. The distribution pattern of fishes in 6 inlet rivers around Lake Biwa was examined during 2011–2012, with 32 and 26 fish species/ subspecies being recorded in autumn and spring, respectively. The relationships between presence/absence of these species and 21 physical environmental factors were analyzed by generalized linear mixed model, the results for 12 species in autumn and 4 species in spring being appropriate for predictability. Distance from the river mouth and number of dams from the river mouth were significant variables for Plecoglossus altivelis altivelis and Cottus reinii in autumn, suggesting that both species were influenced by dams. However, riparian plants were significant for Lake Biwa trout (Oncorhynchus sp.) in autumn, suggesting an important “shelter” component. Furthermore, water quality, including electrical conductivity and dissolved organic carbon, were significant for Tribolodon hakonensis in autumn. Other environmental conditions were more important for a number of other species. Clearly, active conservation of the inlet river environments and their continuity with Lake Biwa is necessary.
