Currently, there is an increase of diversity in the design of complex hydraulic structures. Thus there is a need to establish adequate mathematical models and software with complete description of processes. These models should be focused on certain classes of problems, which statements may change during the simulation. So, in our opinion, so-called self-organizing simulation models are perspective, they adapt to changes in the operating practice of the objects that require rapid adjustments in the boundary conditions and the field of simulation. Results of development of self-adapting complexes of numerical models, permitting calculation of complex water passageway systems with varying flow regime on separate parts (discharge; movement on the dry bottom, provided hydraulic head in free-flow downstream tunnel etc.). Presented system traces the movement of modeling area boundaries (when filling and dumping water passage sections) and chooses the appropriate boundary condition with changing flow regime on the border of modelling area of the flow (free-flowing weir – drowned weir). Given results of numerical simulation of real systems make it possible to consider proposed approach as efficient.