The management of water quality and fishery resources with a major environmental problem in eutrophic coastal sea is studied. The numerical experiments using the water-sediment quality model (WSQM) were carried out for the management of water quality at the Seto Inland Sea in Japan. The results of long-term water quality simulation showed responses of seawater quality to input loads to vary in different localities. A formula roughly forecasting water qualify to estimate the effect of loading abatement was proposed. The simulation for the improvement of seawater quality showed the abatements of nutrient loads such as total phosphorus (TP) and total nitrogen (TN) as well as organic loads such as chemical oxygen demand (COD) to be peformed in the eastern Seto Inland Sea from Bisan Seto to Osaka Bay. On the other hand, it is indicated that the increase of loading leads to the increase of primary production. while not straightly to the increase of fish production for the catch of fisheries.