A transitional separation bubble on the suction side of an SD7003 airfoil is considered. The transition process that forces the separated shear layer to reattach seems to be governed by Kelvin–Helmholtz instabilities. Large scale vortices are formed due to this mechanism at the downstream end of the bubble. These vortices possess a three-dimensional structure and detach from the recirculation region, while other vortices are formed within the bubble. This separation of the vortex is a highly unsteady process, which leads to a bubble flapping. The structure of these vortices and the flapping of the separation bubble due to these vortices are temporally and spatially analyzed at angles of attack from 4° to 8° and chord-length based Reynolds numbers Rec = 20,000–60,000 using time-resolved PIV measurements in a 2D and a 3D set-up, i.e., stereo-scanning PIV measurements are done in the latter case. These measurements complete former studies at a Reynolds number of Rec = 20,000. The results of the time-resolved PIV measurements in a single light-sheet show the influence of the angle of attack and the Reynolds number. The characteristic parameters of the separation bubble are analyzed focusing on the unsteadiness of the separation bubble, e.g., the varying size of the main recirculation region, which characterizes the bubble flapping, and the corresponding Strouhal number are investigated. Furthermore, the impact of the freestream turbulence is investigated by juxtaposing the current and former results. The stereo-scanning PIV measurements at Reynolds numbers up to 60,000 elucidate the three-dimensional character of the vortical structures, which evolve at the downstream end of the separation bubble. It is shown that the same typical structures are formed, e.g., the c-shape vortex and the screwdriver vortex at each Reynolds number and angle of attack investigated and the occurrence of these patterns in relation to Λ-structures is discussed. To evidence the impact of the freestream turbulence, these results are compared with findings of former measurements.