Offshore site investigation is time-consuming and relatively expensive compared to onshore site investigation, because it is affected by severe weather conditions and has low accessibility from the land. Due to these economic and spatial-temporal constraints, it is essential to integrate the available site investigation information for the planning and design of offshore infrastructures. In this study, a GIS-based system was developed to manage and utilize the offshore site investigation data using opensource software. The system mainly performs the function of modeling the geo-information in three dimensions based on the offshore site investigation database. Through the input module, borehole data, geophysical survey data and numerical terrain information are standardized and stored in the database. The three-dimensional spatial modeling module performs outlier analysis of borehole data, subsurface geo-layer stratification, and interpolation of geotechnical properties. For the geo-layer stratification, the geostatistical integration method of borehole and geophysical datasets is adopted as well as conventional geostatistical methods. The optimization method of the results from geostatistical conditional simulation can be used for three-dimensional modeling of geotechnical property. The geoinformation predicted by the analysis module is inserted back into the database. Although this system is designed for offshore site investigation information, it can be used to manage inland and onshore site investigation information. Three-dimensional spatial modeling of site investigation information of an expressway construction site in South Korea was carried out using the developed system and its applicability was verified.