Large scale particle image velocimetry (LSPIV) has become a reliable and accurate technique to measure water surface velocity field in open channels and rivers. The LSPIV technique is based on a camera view framing the water surface, complemented with image-processing methods to compute water surface displacements between consecutive frames. Using LSPIV, high flow velocities, such as flood conditions, are accurately measured, whereas determinations of low flow regimes is more challenging, especially in the absence of floating material carried by the stream. In fact, in unseeded conditions, typical surface feature dynamics must be taken into account. Indeed, besides surface structures advected by the current, capillary-gravity waves propagate on the surface, with their own speed and direction. In this study, the discrimination between these phenomena is discussed, providing a new method to distinguish and to correct unseeded LSPIV measurements with capillary-gravity wave dynamics. Current velocity obtained with such a correction at low flow speed in an artificial channel and in a natural river is in fair agreement with reference observations indicating the need of accounting for the speed and direction of capillary-gravity waves on the surface to obtain reliable measurements of the current vector field, and, as a further result, of the flow discharge over a river cross-section.