Neutron activation analysis was performed on sediments taken from the 250 m thick sediment bed of Lake Biwa, which is composed entirely of lacustrine clay and records paleo-environmental change over the past 430,000 years. A comparison is made between the geochemical compositions of cores from the center of Lake Biwa, and lacustrine surface and terrestrial sediments from around Lake Biwa, to estimate past changes in sediment sources. Time series of Th/Sc ratios are synchronized with glacial–interglacial climatic change and also correlated with the reported aeolian quartz flux data. Th/Sc ratios during the δ 18O stages 1, 5, 7, 9 and 11 are approximately 1.1–1.2, whereas Th/Sc ratios during the δ 18O stages 2, 4, 6, 8 and 10 are approximately 1.0–1.1. The possibility of a contribution from the mafic area in the northwestern shore of Lake Biwa, which has low Th/Sc ratios (ca. 0.8), is excluded by the Ti/Al ratio data. As aeolian dust flux to the downwind area from the Asian desert area is higher during glacial times, this data suggests that aeolian dust reaching Japan has an unexpectedly low Th/Sc ratio of source material, and/or that there was a large shift in the amount of dust flux. This assumption remains to be tested by future studies. Th/Sc ratios apparently lag ca. 5000 years behind the marine δ 18O record during the stage 1 2 , 3 4 , and 5 6 transitions, which coincides with the aeolian quartz flux variation. Continuous increase of Hf contents from ca. 200,000 years BP could be mainly related to upheaval of the Hf rich and high Th/Sc ratio granite block on the west shore of drilling site by active fault movement. The variations in delivery of high Th/Sc granitic debris has damped the oscillation between Th/Sc ratios of sediments and aeolian dust flux during oxygen isotopic stages 2–3. Both the intermittent increase of Na contents from ca. 430,000 years BP to present, and the abrupt increase of Na content at ca. 140,000 years BP are probably due to the subsidence of the northern basin, as the result of tectonic movement around Lake Biwa.