Gabčíkovo Water Structure is a crucial water structure in terms of hydropower and navigation on the Slovak part of the Danube River. Navigation and hydropower are coupled and therefore solved together on the Gabčíkovo Water Structure and Danube river under the Expert Control System (ECS). ECS has two models: Optimization Model and Simulation Model. Optimization Model controls filling and emptying process of the navigation ship lock at the Gabčíkovo Water Structure. In order to perform this process, the software had to be based on theoretical analysis of the relationships of individual physical quantities and parameters expressed by mathematical apparatus. Simulation Model controls discharges and water level regime with respect to navigation safety requirements on the entire section of the Danube river affected by the operation of the Gabčíkovo Water Structure. The software tool for such a complex hydraulic process that would be able to evaluate the impact of the operation had to be developed. The paper describes the principles on which both software work. ECS is a part of the Gabčíkovo Water Structure upgrade and modernization project.