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A mathematical model for simulating water flows with non-uniform sediment transport is proposed based on the shallow water approximation and a multi-layer representation of sediment. The model includes a variety of physical processes: sediment deposition and entrainment; suspended and bed load transport; bed motion caused by the appearance of high slope angles (greater than the natural one); effects of saltation, transition to high Froude numbers, armoring and cross-circulation. The results of the model validation are presented based on laboratory experiments and observations of flows in real rivers. The following problems are considered: the silting and hydraulic washing of a desilting basin; the erosion of bank slopes; development of alluvial stream channels; non-cohesive earthen dam breach. Special attention is paid to studying the influence and adequacy of the model parameters. It is shown that the developed model works well in a wide range of parameters and is consistent with the laboratory experimental data. The proposed modeling approaches are built into the authors’ Stream 2D software, used to obtain the presented results. The work was supported by the Russian Science Foundation, project no. 17-77-30006.