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A well-balanced scheme with total variation diminishing Runge-Kutta discontinuous Galerkin (TVD-RK DG) method for solving shallow water equations is presented. Generally, the flux function at cell interface in the TVD-RK DG scheme is approximated by using the Harten-Lax-van Leer (HLL) method. Here, we apply the weighted average flux (WAF) which is higher order approximation instead of using the HLL in the TVD-RK DG method. The consistency property is shown. The modified well-balanced technique for flux gradient and source terms under the WAF approximations is developed. The accuracy of numerical solutions is demonstrated by simulating dam-break flows with the flat bottom. The steady solutions with shock can be captured correctly without spurious oscillations near the shock front. This presents the other flux approximations in the TVD-RK DG method for shallow water simulations.