Development of counter-rotating streamwise vortices in a rectangular channel with onesided wavy surface has been experimentally quantified using hot-wire anemometry. The wavy surface has fixed amplitude of 3.75 mm. The counter-rotating vortices are pre-set by means of a sawtooth pattern cut at the leading edge of the wavy surface. Variations of the central streamwise velocity U c with a channel gap H = 35 mm and 50 mm (corresponding to a Reynolds number from 1600 to 4400) change the instability of the flow which can be distinguished from the velocity contours at a certain spanwise plane. The streamwise velocity contours and turbulence intensity for Reynolds number Re = 3100 and H = 35 mm show the disappearance of the mushroom-like vortices prior to turbulence near the second peak of the wavy surface, while for higher Re, this phenomenon occurs earlier. Under certain conditions, for example, for Re = 4400 and H = 50 mm, the splitting of the vortices can also be observed.