The present study investigates the transport of dilute bubbles by transitional flow in a joining, cross-flow-type T-junction channel geometry with Reynolds numbers at the outlet branch from Re3 = 600 to 1800 and an inlet volume flow rate ratio of 1. Bubbles with diameters between db = 400 and 600 µm are considered. The schematic pattern of the single-phase flow is introduced based on streakline dye visualizations. Complex 3D flow due to the narrow channel design dominates the recirculation area and flow instabilities become important with increasing Reynolds number, which can be observed by the fading of dye intensity. A numerical method is presented with unsteady boundary conditions based on laser Doppler velocimetry measurements. Bubble trajectories are obtained by an Euler-Lagrange approach. Using high-speed shadowgraphy method combined with image processing, bubble sizes were measured, and bubble trajectories were evaluated. Experimental bubble trajectories and numerically predicted bubble positions show good agreement for Re3 = 600, which is also the case with the dye visualization image. For higher Reynolds numbers, measurements of the bubble trajectories are reported and compared to dye visualization images. The increasing flow instabilities influence the bubble transport, resulting in large variations of bubble locations.