An ecosystem model was developed and applied to Atsumi Bay, Japan, to evaluate the effects of reclaiming seagrass beds and creating artificial shallows with seagrass beds to mitigate the effects of the reclamation. The model can demonstrate the ecological mechanisms in the pelagic and benthic ecosystems including seagrass beds and tidal flats. The objectives of the application of the ecosystem model to Atsumi Bay are presented in this book, as well as a discussion of the effects of the reclamation of seagrass beds and the creation of artificial shallows on the water quality in the estuary.