Lake Biwa, the largest lake in Japan, has been affected by eutrophication and climate warming since the 20th century. To examine the effects of these environmental changes on dominant macrobenthos species in Lake Biwa, the density and composition of these organisms were determined monthly from 1966 to 2000 at an offshore station in the lake, and analyzed in terms of various physicochemical factors. Annual mean bottom temperatures at the site generally remained stable (6.1–8.0°C) until 1985, increased from 1985 (6.5°C) to 1990 (8.3°C), and remained high thereafter (7.4–8.3°C). Branchiura sowerbyi dominated the oligochaete community in terms of density and biomass until 1985. Oligochaete density increased after 1986, dominated by B. sowerbyi, Limnodrilus spp., and Tubifex tubifex. Although the increase in macrobenthic density after 1986 was mainly explained by an increase in T. tubifex density (3811–8076 individuals m–2), total macrobenthos biomass was mainly controlled by B. sowerbyi (1.9–9.5 g m–2). Notably, the increase in T. tubifex density roughly coincided with density decreases in the benthic gobid fish Gymnogobius isaza (from 567 tons to undetectable) and the shrimp Palaemon paucidens (from 758 to 142 tons). Jesogammarus annandalei density increased from 1985, roughly coinciding with the decrease in gobid fish. These findings demonstrate the importance of biological interactions such as predation in the succession of dominant macrobenthos species in Lake Biwa.