Abstract: Using Ecopath with Ecosim, a mass-balance trophic model was manipulated to predict temporal responses of community biomasses to the system-scale removal of oyster-culture racks from Tapong Bay, a eutrophic and poorly flushed lagoon in tropical Taiwan. The model predictions were further compared with separate field observations over a period of 2.5 years. The removal of the oysters was predicted to result in increases in most community biomasses. The model predictions approximately matched the trends of the field observations for phytoplankton, zooplankton, detritivorous fish, and detritus after the removal, so providing a trophic explanation for the responses of these communities in the lagoon. The observed biomasses of benthic communities declined, however, probably as a result of a reduction in biodeposition from the oysters. The biomasses of pelagic fish and soft-bottom fish increased, but that of reef fish decreased after the removal. The field observations demonstrated that plankton communities were controlled, but the biomasses of the benthic and fish communities were enhanced by a high density of suspended oyster culture in a eutrophic lagoon.