The reuse of limestone quarry wastes, in the form of limestone crushing products, is today an urgent task of utilizing cheap and economical raw materials in construction that accounts for the production of effective types of carbonate concretes. Along with this, there is a lack of experimental studies of the physical and mechanical properties of these concretes. The article highlights the issues of structural and functional analysis and synthesis that are necessary to create an optimal internal functional structure of an innovation, that is, concretes based on limestone crushing products. The model of the functional structure of carbonate concretes is based on the physical and technological parameters of the carbonate component, which are determined experimentally by a special technique. The article also discusses methods for calculating the above-mentioned parameters using an algorithm for obtaining high-density fine-grained carbonate concretes that meet high operational and technological requirements with increased crack resistance, water-gas, impermeability and durability. This type of concrete is widely in demand in hydraulic engineering and the construction of large-span structures and systems with dynamic loading. This model is a universal algorithm that considers a scientific approach to the design of this type of structural materials.