Computational fluid dynamics (CFD) provides a flexible tool for investigation of separation processes within membrane hollow fiber modules. By enabling a three-dimensional and time dependent description of the corresponding transport phenomena, very detailed information about mass transfer or geometrical influences can be provided. The high level of detail comes with high computational costs, especially since species transport simulations must discretize and resolve steep gradients in the concentration polarization layer at the membrane. In contrast, flow simulations are not required to resolve these gradients. Hence, there is a large gap in the scale and complexity of computationally feasible geometries when comparing flow and species transport simulations. A method, which tries to cover the mentioned gap, is presented in the present article. It allows upscaling of the findings of species transport simulations, conducted for reduced geometries, on the geometrical scales of flow simulations. Consequently, total transmembrane transport of complete modules can be numerically predicted. The upscaling method does not require any empirical correlation to incorporate geometrical characteristics but solely depends on results acquired by CFD flow simulations. In the scope of this research, the proposed method is explained, conducted, and validated. This is done by the example of CO2 removal in a prototype hollow fiber membrane oxygenator.