Automatic large scale soil model generation is very critical stage for earthquake hazard simulation of urban areas. Manual model development may cause some data losses and may not be effective when there are too many data from different soil observations in a wide area. Geographic information systems (GIS) for storing and analyzing spatial data help scientists to generate better models automatically. Although the original soil observations were limited to soil profile data, the recent developments in mapping technology, interpolation methods, and remote sensing have provided advanced soil model developments. Together with advanced computational technology, it is possible to handle much larger volumes of data. The scientists may solve difficult problems of describing the spatial variation of soil. In this study, an algorithm is proposed for automatic three dimensional soil and velocity model development of southern part of the European side of Istanbul next to Sea of Marmara based on GIS data. In the proposed algorithm, firstly bedrock surface is generated from integration of geological and geophysical measurements. Then, layer surface contacts are integrated with data gathered in vertical borings, and interpolations are interpreted on sections between the borings automatically. Three dimensional underground geology model is prepared using boring data, geologic cross sections and formation base contours drawn in the light of these data. During the preparation of the model, classification studies are made based on formation models. Then, 3D velocity models are developed by using geophysical measurements such as refraction-microtremor, array microtremor and PS logging. The soil and velocity models are integrated and final soil model is obtained. All stages of this algorithm are carried out automatically in the selected urban area. The system directly reads the GIS soil data in the selected part of urban area and 3D soil model is automatically developed for large scale earthquake hazard simulation studies.