Tapong Bay, a eutrophic and poorly flushed tropical lagoon, supports intensive oyster culture. Using the Ecopath approach and network analysis, a mass-balanced trophic model was constructed to analyze the structure and matter flows within the food web. The lagoon model is comprised of 18 compartments with the highest trophic level of 3.2 for piscivorous fish. The high pedigree index (0.82) reveals the model to be of high quality. The most-prominent living compartment in terms of matter flow and biomass in the lagoon is cultured oysters and bivalves, respectively. The mixed trophic impacts indicate that phytoplankton and periphyton are the most-influential living compartments in the lagoon. Comparative analyses with the eutrophic and well-flushed Chiku Lagoon and non-eutrophic tropical lagoons show that high nutrient loadings might stimulate the growth and accumulation of phytoplankton and periphyton and therefore support high fishery yields. However, net primary production, total biomass, fishery yields per unit area, and mean transfer efficiency of Tapong Bay were remarkably lower than those of Chiku Lagoon. The lower transfer efficiency likely results from the low mortality of cultured oysters and invasive bivalves from predation or the lower density of benthic feeders constrained by the hypoxic bottom water as a result of poor flushing. This might therefore result in a great proportion of flows to detritus. However, the hypoxic bottom water might further reduce the recycling of the entering detritus back into the food web. In contrast to many estuaries and tropical lagoons, poor flushing of this eutrophic tropical lagoon might induce a shift from detritivory to herbivory in the food web.