Atmospheric dust has wide‐reaching effects, not only influencing climate conditions, but also ecosystems. The eastern region of the Asian continent is one of the largest emitters of dust in the world, and recent economic growth in the region has been accompanied by an increase in anthropogenic emissions. However, the effects of increased Asian dusts on aquatic ecosystems are not well understood. We examined fossil pigments and zooplankton remains from 210Pb‐dated sediments taken from high mountain lakes of Hourai‐Numa and Hachiman‐Numa, located in the Towada‐Hachimantai National Park of Japan Islands, to uncover historical changes in the phyto‐ and zooplankton community over the past 100 years. Simultaneously, we measured the geochemical variables of TOC, TN, TP, δ13C, δ15N, and lead isotopes (207Pb/206Pb, 208Pb/206Pb) in the sediments to identify environmental factors causing such changes. As a result, despite few anthropogenic activities in the watersheds, alpine lakes in Japan had increased algal and herbivore plankton biomasses by 3–6 fold for recent years depending on the surrounding terrestrial vegetation and landscape conditions. Biological and biogeochemical proxies recorded from the lake sediments showed that this eutrophication occurred after the 1990s when P deposition increased as a result of atmospheric loading of dust transported from the Asian continent. The continued increase of anthropogenically produced dust may therefore impart damaging impacts on mountain ecosystems even if they are protected from direct anthropogenic disturbances.