Management of complex distributed systems, at present, is carried out using information systems designed to collect and manage a large amount of heterogeneous information of an organization or institution. The technical component of such information systems is itself a complex distributed system, and information about the location and mutual arrangement of its individual components, as well as the location of the associated infrastructure and main users, is essential for its high-quality functioning. A method of spatial data mining that suggested in this paper, proposed for formalizing the process of creating specialized databases for the implementation (creation) of individual subsystems as part of complex distributed information systems. The results of the application of this method for the construction of one of the subsystems, namely, the subsystem of information support for the management of the technical component of the information system, as part of a complex distributed information system, are presented on the example of the geoinformation system of the Ufa State Aviation Technical University. The proposed approach to intelligent analysis and representation of spatial data, consisting in a formalized description of various thematic data applied to solving specific problems of information management support in complex distributed systems, can be applied to the construction of complex information systems in significantly distributed organizational and infrastructure.