Wind-speed decline is an important impact of climate change on the eastern Asian atmospheric circulation. Although wind does not determine algae biomass in eutrophic lakes, it is a decisive factor in the formation and severity of algae blooms. Based on 2000–2018 MODIS images, this study compared the effects of wind speed on algal blooms in three typical eutrophic lakes in China: Lake Taihu, Lake Chaohu and Lake Dianchi. The results indicate that climate change has different effects on the wind speed of the three lakes, but a common effect on the vertical distribution of algae. A wind speed of 3.0 m/s was identified as the critical threshold in the vertical distribution of chlorophyll-a concentrations in the three study lakes. The basic characteristics of the periodic variation of wind speed were different, but there was a significant negative correlation between wind speed and floating algal bloom area in all three lakes. In addition, considering lake bathymetry, wind direction could be used to identify locations that were particularly susceptible to algae blooms. We estimated that algal bloom conditions will worsen in the coming decades due to the continuous decline of wind, especially in Lake Taihu, even though the provincial and national governments have made major efforts to reduce eutrophication drivers and restore lake conditions. These results suggest that early warning systems should include a wind-speed threshold of 3.0 m/s to improve control and mitigation of algal blooms on these intensively utilized lakes.