The interplay of heat and mass transfer in a gas/liquid/solid or heterogeneous catalytic microreactor, in which bubbles grow on a surface, is highly complex. Specifically, distortion of the fluid due to the protrusion and the location of the bubbles can affect transport phenomena, and, in turn, the chemical conversion. Therefore, understanding nucleation and growth of bubbles within microreactors is desirable to optimize reactor performance. A promising approach to that end, and to ultimately control transport phenomena in multiphase catalytic microreactors, is to direct the nucleation of bubbles. For this purpose, we report here a microfluidic device that contains hydrophobic micropits along the smooth floor of a rectangular cross-section microchannel, which were patterned in a silicon substrate using deep reactive ion etching. The pits are intended to act as nucleation sites. Device performance was evaluated for the two cases of boiling of water and outgassing of dissolved carbon dioxide (CO2). As intended, bubbles were observed to form at the micropits, but also along the rough microchannel side walls. Confocal microscopy revealed that bubbles had spherical shapes, and formed a contact angle with the microchannel floor of >90°. The experimentally determined bubble geometry was used as the boundary condition for a 3D-numerical model. Numerical simulations indicated that the presence of bubbles had a large impact on the local flow distribution, concentration field and reaction conversion within the microreactor, and therefore on the overall conversion for a chosen model reaction.