This paper presented a two-dimensional, well-balanced hydrodynamic and sediment transport model based on the solutions of variable density shallow water equations (VDSWEs) for sediment-laden flows, and the Exner equation for bed changes. Those equations are solved in a coupled way by the first-order Godunov-type finite volume method. The Harten-Lax-van Leer-Contact (HLLC) Riemann solver is extended to find the local Riemann fluxes in order to maintain the exact balance between the momentum term and the bed slope term. The advantage of a well-balanced scheme over an unbalanced scheme is demonstrated by the synthetic standing contact-discontinuity test case. Then, the model is employed to simulate two laboratory experiments. At last, a field case, the 1996 Lake Ha! Ha! flood event (Canada), is simulated. Results of cross sectional geometries and profiles of longitudinal thalweg agree well with measurements. The accuracy and simplicity of the numerical model, together with the robust implementation, make the model a good candidate for practical engineering applications.