In 1950’s and 1960’s, Mihama beach in Heda Bay located on western coast of Izu peninsular had been famous for the richness in shell fauna, for example, about 400 species including rare ones were collected. In 2000’s, however, the impoverishment of ecosystem function has become considerable, which led us to project the investigation on the origin and restoration. The authors carried out field survey in 2007–2008 and found that the impoverishment of Mihama is derived not from surface water but from the benthic environment. The measured water current at the site was quite small, which indicated the water exchange was very weak. It must be one of the main causes of unfavorable benthic environment. Thus environmental regeneration plans for Mihama was proposed in which the pears blocking the water current be removed. In order to assess the effect of proposed plans, simulation-based habitat evaluation was conducted. A three-dimensional hydrodynamic and sediment transport models were developed to reproduce the characteristics of currents and predict the sediment size around Mihama. For the assessment of the ecological status, HEP (Habitat Evaluation Procedure) was employed, in which one of the typical species of bivalves is chosen as a target species. Water depth, sediment size, friction velocity at the bottom, etc. were considered as the environmental factors for the target species. The suitability indices (SI) for each environmental factors were calculated by using the results of hydrodynamic and sediment transport simulations. By using the developed scheme, total habitat unit was evaluated for the proposed regeneration plans and compared to that without countermeasures. It was predicted that the removal of the piers will improve the habitat condition in the target site. Based on the proposal by the authors, a water pathway under the pier was built in 2009. The authors conducted field survey again in 2014 and confirmed that the benthic environment has been improved.