This paper is devoted to the problem of modeling data and processes in big data systems including polystorages and other heterogeneous components of information processing. At present, approaches to harmonization of polystorages data models are proposed in this research area. Various proposed methods are considered in this paper, but these solutions are not suitable for use in information security problems directly. The authors formulate requirements for modeling of the considered objects for solving security problems and formulate a level approach to modeling based on the general concept of poly-storage security within the framework of the consistency approach. The paper presents an original systematization of data models of modern poly-storages and DBMS in their composition, taking into account the used mathematical apparatus. A new methodology of three-level modeling of data and processes in the object of protection is proposed, the bases of models for all levels of data representation are formulated. The results of the work lay the foundation for the complex representation of data and processes in solving the problems of security and analyzing the security of big data systems.