A new methodology for estimating the discharge starting from the monitoring of surface flow velocity, usurf, is proposed. The approach, based on the entropy theory, involves the actual location of maximum flow velocity, umax, which may occur below the water surface (dip phenomena), affecting the shape of velocity profile. The method identifies the two-dimensional velocity distribution in the cross-sectional flow area, just sampling usurf and applying an iterative procedure to estimate both the dip and umax. Five gage sites, for which a large velocity dataset is available, are used as a case study. Results show that the method is accurate in simulating the depth-averaged velocities along the verticals and the mean flow velocity with an error, on average, lower than 12% and 6%, respectively. The comparison with the velocity index method for the estimation of the mean flow velocity using the measured usurf, demonstrates that the method proposed here is more accurate mainly for rivers with a lower aspect ratio where secondary currents are expected. Moreover, the dip assessment is found more representative of the actual location of maximum flow velocity with respect to the one estimated by a different entropy approach. In terms of discharge, the errors do not exceed 3% for high floods, showing the good potentiality of the method to be used for the monitoring of these events.