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OGC Open Modeling Interface (OpenMI 2.0) standard was used to develop an integrated hydrological modeling system, which combines the semi-distributed hydrological model ECOMAG with the hydrodynamic model Stream-2D. The OpenMI is a data exchange protocol to facilitate communication of numerical models operating at different time-spatial scales, databases and visualization tools. The ECOMAG model describes hydrological processes at a river basin scale including the processes of snow accumulation and melting, soil freezing and thawing, water infiltration into unfrozen and frozen soil, evapotranspiration, thermal and water regime of soil, overland, subsurface and groundwater flow. The Stream-2D model is based on two-dimensional hydrodynamic equations and describes spatial distribution of water flow velocity and depth, flood inundation dynamics and other processes within a floodplain-channel system. In this study, we demonstrated ability of the developed modeling system to be used as a flood risk management tool for analyzing flood protection effect of large reservoirs and large-scale hydro-technical constructions (such as dikes and bank reinforcements) on populated floodplains. The case study was carried out for the middle Amur River where large reservoirs are currently located on the Zeya and Bureya tributaries. The system was calibrated and validated against the available observation data at the study basin and demonstrated good performance. Numerical experiments were carried out with the modeling system in order to reproduce flood regime near the city of Blagoveshensk under different scenarios of location of existing and projected flood protection infrastructures.