We have developed an operational oceanographic system for the southern coastal waters of Korea as a part of the development of Korea Operational Oceanographic System (KOOS). The operational oceanographic system consists of atmospheric and hydrodynamic models coupled with three-dimensional hydrodynamics, wave, sediment transport and water quality modules. The forecasting system focuses on the southern coastal waters of Korea which are very shallow with complex coastal lines and hundreds of islands. The operational modeling system of the southern coastal waters of Korea uses 3-D operational model ROMS (Haidvogel et al., 2008) which is 2-way coupled with SWAN for waves, nested with WRF for meteorological surface forcing, internally linked with sediment transport (Warner et al., 2008), and externally linked with CE-QUAL-ICM (Cerco and Cole, 1993, Kim et al., 2011) for water quality etc. The forecasting system provides predicted oceanographic data and warning of storm surge occurrence two times a day in the 72-hours base for the public through a web-GIS based coastal information system.