Three-dimensional earth sciences information is being made available in digital formats because such information is useful and understandable to various users. In this study, we develop a three-dimensional hydrogeological model of Tsukuba City and the surrounding region, and develop a method for estimating the hydraulic conductivity of aquifers in combination with the three-dimensional hydrogeological model and other related hydrogeological information with the primary objective of proposing a method for evaluating groundwater resources. The three-dimensional hydrogeological model was developed using a geological map and drilling data with data interpolated using a geostatistical method. The model developed reproduced the data used well, and it was found to be accurate for practical use. Moreover, this model could be used for various types of visualization, from which information could be extracted and applied immediately to numerical simulations; this provided information that was useful and understandable for evaluating groundwater resources. The proposed method for estimating the hydraulic conductivity of aquifers was developed from hydraulic conductivities obtained from various drilling surveys, which were grouped together taking geology and stratigraphy into consideration based on a three-dimensional hydrogeological model, and using a statistical analysis. This method can be used to rapidly evaluate trends in hydraulic conductivity by integrating data distributed over a broad area. In addition, if a columnar section of an evaluated point is obtained, this method can be used to determine the actual hydraulic conductivity of aquifers. Therefore, these methods were found to be effective for evaluating groundwater resources.