Both geometric (bathymetric) and hydrographic (ambient discharge) data should be used for defining the appropriate rectangular cross-section. A schematization may be quite evident for well-channeled and regular rivers or artificial channels. For highly irregular cross-sections, it may require more judgment and perhaps several iterations of the analysis to get a better feel on the sensitivity of the results to the assumed cross-sectional shape.
Be aware that a particular flow condition such as a river discharge is usually associated with a certain water surface elevation or "stage." Data for a stage-discharge relationship is normally available from a USGS office; otherwise it can be obtained from a separate hydraulic analysis or from field measurements.