Stream flow records and irrigation delivery and return flows are typically estimated with the use of stage-discharge ratings. These ratings may be for channel control or for measurement structures. The conventional rating method relates stage to discharge; however, at sites prone to flow reversals, changes in stream bed roughness, backwater, or tidal effects, the relation between stage and discharge is not unique and a velocity-index rating is often developed. A velocity-index rating relates the mean velocity in the cross-section to an index-velocity determined from velocity measurements at defined locations in the cross-section. Application of velocity index ratings assumes that the relation between the measured index velocity and the mean velocity in a cross-section is constant. This assumption is not valid if the channel experiences significant flow disturbances. This paper presents a virtual flow meter developed to evaluate the effect of hydraulic factors such as vegetation growth, obstacles, variable backwater, etc. on the stability of velocity-index ratings for different instrument and measurement configurations. A three-dimensional computational fluid dynamics (CFD) model was used to simulate velocity distributions that would result from various flow and channel conditions modeled. The virtual flow meter allowed for different instrument configurations (i.e., number of acoustic beams, angle between beams, orientation of instrument, location of instrument, etc.) by specifying an instrument configuration and then sampling the simulated velocity field at locations based on the specified configuration. The index velocities sampled by the virtual flow meter and the mean velocity at the cross-section were used to develop velocity-index ratings and examine the effect of changing hydraulic factors on the uncertainty in the discharges determined from the rating. The analytical tool described in this paper provides insight to both the effect of changes in flow and channel conditions, as well as changes in instrument configuration, on velocity-index ratings.