We proposed a biological contamination control technology that preyed on and removed only invading weed algae by introducing rotifers into the culture ponds of Botryococcus braunii that had enlarged colonies. Botryococcus braunii strains Showa and Sanshiro belonging to race B were used, and the colonies were grown on a high-salt medium containing 3 g L−1 NaCl. Brachionus calyciflorus, a freshwater rotifer with large prey size, was used as the predator, and Westella sp. was used as the model weed algae. In the mixed culture of B. braunii and B. calyciflorus, the growth rate of B. braunii cultured in Chu13, a freshwater medium, was reduced due to predation by B. calyciflorus. However, enlarged B. braunii cultured in a high-salt concentration medium escaped predation and maintained a growth rate equivalent to or higher than that of the control. In the three trials combining B. braunii, B. calyciflorus, and Westella sp., B. calyciflorus was initially applied such that the ratio of the number of rotifers to the algal density of Westella sp. was 2.0 × 10−6. Under these conditions, the initial growth of Westella sp. was suppressed when using the Showa strain, which showed significant growth. The larger colony size of the Sanshiro strain showed greater proliferation of Westella sp. because its optical density was lower than that of the Showa strain. The growth of the Sanshiro strain was suppressed until day 6, when predation reduced Westella sp. density, but the growth rate recovered thereafter. A model for the optimum number of rotifer inputs, considering the optical density and the number of rotifers remaining in the future, and technology for outdoor cultivation must be developed in the future. We demonstrated the potential of an eco-friendly weed-algae-removal technology that uses a predation ecosystem without using special culture environments or pesticides.