A three-dimensional model in which the effects of buoyance and wave are considered is developed to demonstrate how the tendency of algae to move, coupled with wind-induced circulation, leads to horizontal and vertical heterogeneity in algae concentration in Taihu Lake. Results show that the distribution of algae will be different depending on whether the windspeed is higher or lower than the critical windspeed. If the windspeed is lower than the critical one, algae may migrate toward the downwind end of the lake and accumulate there. The floating algae are expected to remain on the surface. But above the critical windspeed, water surface becomes rough and waves take place. in that case, interactions between wind-generated turbulence, mean currents and waves cause algae to leave away from the water surface, so surface accumulation of algae do not occur again. in summer, the algae of Taihu Lake migrate with southeast wind toward the northwest region of the lake and then form blooming there for low windspeed; but when the windspeed above the critical value, the wind-generated waves may impress the accumulation of algae and make algae distribute more uniformly in the lake. This result is verified by the observed data of Taihu Lake.