Hydrodynamic and sediment transport modeling is important to the analyses of the aggradation and degradation of a river system, the sediment management in a reservoir, and the study of downstream effect on the coastal sediment. This paper presents a development of a three-dimensional hydrodynamic and sediment transport model to investigate the variation of sediment concentration in Shihmen Reservoir in Taiwan under typhoon induced flood events. The fundamental equations that govern fluid flows and sediment concentration are the Reynolds-averaged Navier-Stokes (RANS) equations and sediment transport equation. Model equations are solved by using an implicit, finite-difference scheme in a curvilinear and vertically stretched coordinate system. A case study of Shihmen Reservoir utilizing the present flow and transport model is presented. The upstream flow-rate conditions are obtained from the data recorded during the 2005 Typhoon Haitang. The computed results clearly reflect the three-dimensional feature of the velocity field in the reservoir. The predicted time-varying water surface elevation during the 140-hour flood event agrees well with measured data. For the sediment concentration, only limited measurements in the domain are available. When comparing with the measured data, the present model is capable of providing reasonable predictions on the rising trend of sediment concentration during the period that flow rate increases, however, the model overestimates concentration values at the recession stage when the measurements of sediment concentration are shown in the decreasing trend. Other results showing the time variation of the velocity vectors and sediment concentration at selected vertical layers are presented and discussed.