A three-dimensional Computational Fluid Dynamics model is built for a commercial Atomic Layer Deposition (ALD) reactor, designed to treat large area 20 cm substrates. The model aims to investigate the effect of the reactor geometry and process parameters on the gas flow and temperature fields, and on the species distribution on the heated substrate surface, for the deposition of Al2O3 films from trimethyl aluminum and H2O. The investigation is performed in transient conditions, without considering any surface reaction. A second CFD model is developed for the feeding system of the reactor, in order to calculate the unknown reactant inlet flow rates. The two models are coupled via a computational strategy dictated by the available experimental measurements. Results show that a purging flow entering the reactor through its loading door affects the flow field above the substrate surface and causes non-uniformity in the temperature and reactants concentration on the substrate surface. During the TMA pulse, a recirculation sets in above the substrate surface, leading to a non-uniform distribution of species on the surface.