We combine non-hydrostatic flow simulations of the free surface with a discharge model based on elementary gate flow equations for decision support in the operation of hydraulic structure gates. A water level-based gate control used in most of today's general practice does not take into account the fact that gate operation scenarios producing similar total discharged volumes and similar water levels may have different local flow characteristics. Accurate and timely prediction of local flow conditions around hydraulic gates is important for several aspects of structure management: ecology, scour, flow-induced gate vibrations and waterway navigation. The modelling approach is described and tested for a multi-gate sluice structure regulating discharge from a river to the sea. The number of opened gates is varied and the discharge is stabilized with automated control by varying gate openings. The free-surface model was validated for discharge showing a correlation coefficient of 0.994 compared to experimental data. Additionally, we show the analysis of computational fluid dynamics (CFD) results for evaluating bed stability and gate vibrations.