This research estimated stream discharges indirectly by hydraulic channel routing. Only stage data from three stage stations and river cross section data were used to estimate Manning roughness coefficients and to compute stream discharges. When the discharges were estimated a stage-stage set of conditions was used for upstream-downstream boundary conditions. The research used the data from the upper Mississippi River. The hydraulic channel routings were performed by DWOPER (operational dynamic wave model). The global optimization program of SCE-UA was used to improve the roughness coefficient estimation module of the modified Newton-Raphson method in DWOPER. The results from SCE-US were better. For the case study of a flood, most estimated discharges except a few show errors within 10%.