Mathematical modeling of the Cheboksary reservoir using one-dimensional numerical model combined with GIS-technology was used to solve the following practical problems: prediction of water levels during the breakthrough wave passage and at the same time the boundaries of flood zones of settlements; analysis of the situation in the water body at the design and operation of hydraulic structures; development of measures to eliminate emergencies; conservation of water resources from exhaustion and environmental protection.In the calibration, measurements at the hydrological stations for 2001-2012 were used. Using the constructed and calibrated model the analysis of inundation zones as a result of dam break at different NPP at Cheboksary hydroscheme was carried out. Practical value of the work: the obtained research of joint use of GIS technologies and computational hydrodynamic programs allows improving methods of simulation modeling of regulated means.