Sediment deposition is a serious issue in river channels, especially at river confluences. Massive sediment deposition triggered by flow stagnation causes changes in riverbed cross-section and morphology. The capacity of the river cross-section decreases along with the increase in sediment deposition in the area. This paper aims to simulate sediment transport at the confluence of the Palu and Sombe-Lewara Rivers, one of the rivers with sedimentation issues in Central Sulawesi, Indonesia. The simulation is performed with the HEC-RAS2D Model to predict sediment transport rates and bed morphology changes due to flooding. Supporting data for this model are discharge data transformed from rainfall data with a return period of 50 years, DEM data generated from field measurement data, and sediment grain gradation data obtained from sieve analysis of field sediment samples. The formation of mesh/grid as the basis for numerical modeling is performed on the RAS Mapper module based on DEM data of the study area. The DEM resolution is a reference in determining the mesh/grid distance which will ultimately affect the accuracy of predictions of water level, sediment transport and bed morphology changes. Calibration has also been done in previous studies by assessing observed and simulated water levels and obtaining the optimal Manning roughness coefficient of 0.037. The results of the study indicate that the flow velocity is distributed in the transverse direction at the river confluence. The velocity increases on the left and right sides of the stagnation line, respectively reaching 3.5 m/sec and 5.7 m/sec at discharge in the Sombe Lewara River of 40 m3/sec and 650 m3/sec in the Palu River. Furthermore, the velocity gradually decreases towards the river bank along with the decreasing influence of secondary currents. The sediment transport rate at the river confluence is 0.21 m3/sec and 1.45 m3/sec respectively, comparable to the sediment supply from the upstream catchment. The sedimentation pattern follows the velocity distribution where the riverbed is graded on the left side of the flow stagnation line reaching 1.2 m.