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Anthropogenic aerosol increases over the past few decades have weakened the Asian summer monsoon(1-3) with potentially far-reaching socio-economic and ecological repercussions. However, it is unknown how these changes will affect freshwater ecosystems that are important to densely populated regions of Asia. High-resolution diatom records and other proxy data archived in lake sediment cores from the Chinese Loess Plateau allow the comparison of summer monsoon intensity, lake trophic status and aquatic ecosystem responses during warming periods over the past two millennia. Here we show that an abrupt shift towards eutrophic limnological conditions coincided with historical warming episodes(4,5), marked by increased wind intensity and summer monsoon rainfall leading to phosphorus-laden soil erosion and natural lake fertilization. In contrast, aerosol-affected Anthropocene warming catalysed a marked weakening in summer monsoon intensity leading to decreases in soil erosion and lake mixing. The recent warm period triggered a strikingly different aquatic ecosystem response with a limnological regime shift marked by turnover in diatom species composition now dominated by oligotrophic taxa, consistent with reductions in nutrient fertilization, reduced ice cover and increased thermal stratification(6). Anthropogenic aerosols have altered climate-monsoon dynamics that are unparalleled in the past similar to 2,000 years, ushering in a new ecological state.