A fatal flood disaster due to levee breach of Kariyata River occurred in the Chuetsu area of Niigata Prefecture on 13 July 2004. Many houses were swept away and substantial areas of Sanjo City, Mitsuke City and Nakanoshima Town were flooded by muddy water. Removal of mud and other sediment deposits in residential areas in the aftermath of the flood was difficult. To better understand and prevent flood disasters, a two-dimensional numerical model for unsteady flow and non-uniform sediment transport was developed using the finite difference method on a staggered grid. The model consists of two main components: (1) a simplified hydraulic scheme that predicts floodwater flow depth and velocities; and (2) a sediment transport scheme that simulates multi-class sediment accumulation. The sediment model addressed the dominant process of sediment transport, settling, deposition and resuspension, and bed changes in the flooded regions around the break point on the Kariyata River. The model was calibrated using a combination of field data and calibration parameters derived from the existing literature. The simulated results show good agreement with field data.