The problem of studying the dynamics of elements of hydro-technical structures interacting with fluid is considered in the article. On the basis of Lagrange’s variational principles, the basic equations are obtained that characterize the dynamics of complex, multiply connected structurally non-homogeneous shell systems interacting with flowing fluid. Dynamic equations of a cylindrical shell are obtained. To determine the fluid pressure on the shell surface, a boundary value problem based on the laws of hydroelasticity was used. A software package was developed for studying the dynamic characteristics of complex, multiply connected structurally non-homogeneous shell structures, as well as programs for studying the dynamic characteristics of a composite structure using the orthogonal sweep method. Dynamic characteristics are determined for different levels of water filling.