We investigate transport effects on in situ studies of defined model catalysts using a multi-scale modeling approach integrating first-principles kinetic Monte Carlo simulations into a fluid dynamical treatment. We specifically address two isothermal flow setups: (i) a channel flow with the gas-stream approaching the single crystal from the side, as it is representative for reactor scanning tunneling microscopy experiments and (ii) a stagnation flow with perpendicular impingement. Using the CO oxidation over RuO2(1 1 0) as showcase, we obtain substantial variations in the gas-phase pressures between the inlet and the catalyst's surface. In the channel geometry, the mass-transfer limitations lead furthermore to pronounced lateral changes in surface composition across the catalyst's surface. This prevents the aspired direct relation between activity and catalyst structure. For the stagnation flow, the lateral variations are restricted to the edges of the catalyst. This allows to access the desired structure-activity relation using a simple model. (C) 2012 Published by Elsevier Inc.