Multi-wafer viscous flow reactors have been already used to enhance throughput of atomic layer deposition (ALD) processes. In this work, simulation of three-dimensional multicomponent flow inside a multi-wafer reactor integrated with surface reactions was performed to understand the effects of configuration of wafers on film depositions. The simulations were performed at a fixed operating pressure and temperature of 10 torr (1333 Pa) and 300 °C, respectively, using Ansys Fluent. The distance between the wafers and the inlet manifold of the reactor was found as a key parameter that affects the initiation of deposition. Interactions between the generated gas from surface reactions due to depositions on wafers at different levels play an important role for concentration of reactant over the wafers and, in turn, deposited film thickness. The results will be beneficial for designing multi-wafer reactors to minimize the delay in initiation of depositions and reduce the overall duration of high throughput ALD processes.