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In the present work, a modified numerical model was developed to simulate the water flow during a dam break with the mud layer transfer of different heights, consisting of three phases (water, air, and a phase for deposition). To carry out a numerical simulation of this process, a mathematical model based on the VOF (volume of fluid) method was modified, taking into account the movement of the water-free surface, which is carried out by the movement of water flow based on the Newtonian fluid model, and the movement of mud impurities is based on the non-Newtonian fluid model. Validation of the constructed model for the influence of three-dimensional features of the flow on morphological changes is carried out by a modified mathematical model and compared with the results of calculation for two-dimensional (2D) and three-dimensional (3D) models. The proposed method for modeling is applied on a real complex terrain, which was based on the Kargalinka – a river in Almaty and the Almaty region of Kazakhstan, the right tributary of the Kaskelen River. Simulation analysis is carried out for cases with different deposit heights. All results of the numerical simulation can be visually viewed using graphs and illustrations. [ABSTRACT FROM AUTHOR]