Ecopath with Ecosim (EWE) modeling software was used in constructing steady-state trophic models of three diverse seagrass ecosystems to analyze the impact of biomass changes in each component of the ecosystems. The food web models were utilized to make predictions and management options regarding the impacts of biomass alterations in three varied actual scenarios: (1) pristine, isolated, and sheltered seascape; (2) increased connectivity with mangroves; and (3) increased connectivity with corals. The Mixed Trophic Impact (MTI) analysis was utilized to identify consumer compartments' cumulative effects on the producer compartment (i.e., seagrass). The stability and resilience of the seagrass systems were inferred from the network flow indices as the biomass functions. Then, the models were subjected to multiple dynamic simulations. The hypothesis is that the three different scenario simulations resulted in varied biomasses and trophic interactions that revealed insights towards possible management options of the seagrass systems in Caramoan Peninsula, Philippines. Results revealed that although all the seagrass systems are immature, the pristine, isolated, and sheltered seascape (Site A, Lipata Bay) should be given more management owing to its vulnerability that the presence or connectivity cannot afford with other ecosystems (e.g., coral reefs and mangroves). The seagrass meadow nearest to the mangrove forest (Site B, Manlawi Bay) needs unique management to maximize its potential as a refuge for crustaceans and other economically important invertebrates. The seagrass meadow closest to the coral reefs (Site C, Hurandayan Bay) can also be considered conservation sentinels since it is less susceptible to stress-induced changes and can recover from unexpected perturbations than the other seagrass meadows.