A field simulation experiment was conducted to test the hypothesis that altering bivalve aquaculture methods could promote the restoration of eutrophic waterbodies. We used three aquaculture methods-benthic aquaculture, suspended aquaculture, and macrophytes/bivalve combined aquaculture-to (1) investigate their effects on seston removal through monitoring water turbidity, pelagic and benthic algae, and (2) compare their impacts on the phosphorus (P) balance at the water-sediment interface by determining different forms of P contents in the water and sediments. The results showed that the seston removal effects did not differ significantly among these three aquaculture methods. Furthermore, the changes of all investigated P parameters in the water and sediments showed that P release occurred in the benthic and suspended aquaculture treatments. The suspended aquaculture strengthened the regeneration of P from sediments into the water compared with the benthic aquaculture. In addition, the results of a principal component and classification analysis showed that macrophytes/bivalve combined aquaculture promoted the maintenance of restoration effects and P balance at the water-sediment interface. In conclusion, benthic aquaculture coupled with replanting submerged macrophytes is a better choice for water managers when using biomanipulation of bivalves to remedy eutrophic waterbodies.