Throughout the development of the hydropower special attention was paid to the formation of a theoretical framework and methods of parameters and operating modes of powerhouses study. Under current design standards mathematical modeling of powerhouse is performed in two-dimensional for the axisymmetric problem. Up to now this method of simulation in Russia is the determining, although it has long lagged behind the capabilities of modern universal software of finite element analysis. The article presents analysis of the mathematical modeling methods for powerhouses of high-head hydroelectric power plants. Statement of the problem of three-dimensional modeling of the object – powerhouse is given. The procedure for multilayer three-dimensional modeling of water-conveyance conduits is presented. Outlined are the advantages of detailed numerical models of powerhouses in the context of their reliability verification.