A method is proposed to control phytoplankton biomass in aquacultural ponds, using both zooplankton and filter-feeding silver carp (Hypophthalmichthys molitrix). The technique maintains co-existence of zooplankton and filter-feeding fish by excluding the fish from part of the water column. Zooplankton, which feed on smaller algal species, and silver carp, which feed on large algae and zooplankton, together can consume all sizes of phytoplankton, thus controlling algal biomass. This technique was tested in 1000-L tanks, some containing channel catfish (Ictalurus punctatus) alone, some both catfish and silver carp, and others catfish and silver carp with a zooplankton refuge. The refuge permitted coexistence of high densities of large zooplankters with the filter-feeding fish. This combination of filter-feeders reduced algal biomass by as much as 99%, increased phytoplankton diversity, and showed a trend toward improved silver carp growth compared with treatments without a refuge. The proposed technique could be applied to both intensive and extensive aquacultural systems.