This study introduces the navigational environment database(DB) compiling water depth, sediment type and marine managed areas (MMAs) in coastal waters of South Korea. The water depth and sediment data were constructed by combining their sparse points of electronic navigation chart and survey data with high spatial resolution using the inverse distance weighting and natural neighbor interpolation method included in ArcGIS. The MMAs were integrated based on all shapefiles provided by several government agencies using ArcGIS because the areas should be used in an emergency case of ship. To test the validity of the constructed DB, we conducted a test application for grounding and anchoring zones using a ship accident case. The result revealed each area of possible grounding candidates and anchorages is calculated and displayed properly, excluding obstacle places.