Large-scale coherent vortices such as separated vortices and kolk-boils are often observed and generated behind crests of sand dunes in fluvial rivers. The kolk-boil vortex greatly affects transport of suspended sediment which develops up to the free surface. In the present study, both visualization by dye-injection technique and turbulence measurements with a laser Doppler anemometer were conducted in order that the elemental structure of vortices could be clarified. 3-D space-time structures of the coherent vortices are discussed by evaluating conventional correlation coefficients and also by using conditional sampling techniques. Instantaneous velocity-velocity combinations at different points were simultaneously measured by means of two sets of laser Doppler anemometers and an automatic traversing system. Refined physical models of coherent vortices are proposed in the present study.