Seawater circulations between a bay and the open sea play an important role to make the ecosystem healthy, providing nutrient and oxygen to the benthic environments and cleaning up pollutions. The health of the benthic environment in a bay is closely related to the flushing characteristics of seawater. In this study, to estimate the seawater distribution and circulation characteristics of benthic environment in the Geunso bay, we calculated the hydraulic turn-over time by a hydro-hypsographic analysis. Digital elevation model (DEM) which was generated using waterline method based upon remotely sensed data and water depth of the subtidal zone estimated by echo-sounding survey was applied to the hydro-hypsograhic analysis through a geographic information system (GIS) spatial analysis. The results showed that 95% of the total area of the bay was tidal flat and the hydraulic turn-over time was 1.03 tidal cycle, which indicated that the flushing characteristics of the Geunso bay was very good. Geunso bay was revealed to occupy relatively wide area of benthic environment and to have relatively big tidal range over other domestic and foreign coastal environment, therefore it could have a better seawater circulation characteristics. This result can be effectively applied as fundamental information to establish the system for a quantitative estimate of health of coastal environment in the west coast of Korea and manage the ecosystem in benthic environments.