Obtaining accurate measurements of river discharge at or above flood stage has long been a challenging and dangerous task in the southwestern United States where flows are flashy and sediment concentrations are high. During recent years, the use of small unmanned aerial systems (sUAS) for measuring discharge has become more common due to increased accessibility and usability. Using the footage collected with the sUASs along with Large Scale Image Velocimetry techniques, a detailed surface velocity distribution can be obtained. This measured velocity distribution is then used to calculate flood discharge when multiplied by the velocity index and the cross-sectional area. Importantly, the quality of the discharge calculation is directly correlated with the accuracy of the velocity index value. Most approaches of selecting the velocity index are qualitative and could be improved by leveraging surface flow characteristics and channel roughness to quantitatively estimate velocity index. To test the veracity of the method, velocity index and discharge were calculated for lined, earthen, and natural channels using the turbulence dissipation rate and channel roughness. The calculated velocity index and discharge measurements were compared with known measurements collected with acoustic doppler current profiler sensors to determine the accuracy of the method. The proposed method achieves discharge estimate errors as small as 2%. The results from this project have the potential to influence the future of techniques and methods used to make flow measurements in the southwestern U.S. as they help unlock the full potential of sUAS measurements.