To illustrate the control of harmful cyanobacterial growth and the removal of nutritients from fresh water, three submerged macrophytes were grown in the raw water of Guishui Lake. Lindernia rotundifolia, Hygrophila stricta, and Cryptocoryne crispatula were grown together in situ to assess their effectiveness in nutrient removal in microcosms. Results revealed the inhibitory effects of these species on cyanobacterial growth. In addition, water quality in the planted microcosms showed improvement when compared to the water quality of the unplanted microcosm. At all treatments studied, the chemical oxygen demand in the planted microcosms was lower than that in the unplanted microcosms, and the removal rate of all the nitrogen and phosphate in the planted microcosms was better than that of the microcosm without plants. Our study offers a useful algal control method for the lakes or reservoirs that suffer from harmful cyanobacterial blooms.