Lyophilization is a form of drying in which water is removed from a frozen product by a sublimation process at low pressure. The product is usually found in vials in pharmacies. After the freezing phase, the ice sublimation process starts when the system pressure drops and heat is supplied from the shelves. Currently, there is a lack of coupled models that would directly allow to evaluate the effects of local hydrodynamic conditions on the drying of the product inside the vial. In this work, a numerical model for the transport phenomena during freeze-drying is presented, where the drying kinetics of a product inside each single vial is simulated with a dedicated 1D product model and a stopper resistance hydraulic model, which are linked to the time-dependent 3D CFD solution of the flow field in the drying chamber. Experimentally determining the drying kinetics of a product is often time consuming and uses expensive ingredients. There also remains the problem of transferring drying cycles between devices of different sizes, since local hydrodynamic conditions may be different. To model the time-dependent drying process, various geometric approximations for vials are used, ranging from 0D models to 1D models to axisymmetric 2D vial models. To evaluate the local hydrodynamic conditions within the lyophilizer, computational fluid dynamics (CFD) is increasingly used to model the process. Examples of such an approach include the numerical models that consider the effects of the geometry and position of the valves, deposition of ice on the cold surfaces of the condenser, and the choked flow. Currently, there is a lack of coupled models that would allow direct evaluation of the effects of local hydrodynamic conditions on the drying of the product in all vials in the drying chamber. In this work, we present a numerical model for the transport phenomena during lyophilization that simulates the drying kinetics of a product in each vial. For this purpose, we use a specific 1D product model coupled with the time-dependent 3D CFD solution of the flow field in the drying chamber. A laboratory type freeze dryer model Kamenik et al. (2022) was used with two shelves installed. As can be seen from the calculated local pressure distribution across the shelf, there are significant local pressure differences between vials. The pressure is highest in the centre of the shelf and decreases toward the sides of the shelf. As can be seen, pressure differences are observed that significantly affect the pressure difference between the sublimation front and the drying chamber under the targeted conditions of the low-pressure system, resulting in lower mass flow rates for the vials in the middle shelf positions and longer drying times. The computational results of the 1D model coupled with the 3D model CFD show that the model is able to resolve variations in the local pressure conditions in the chamber and the local kinetics of vial drying at different scales. The modelling approach provides a reliable digital twin for the lyophilization process.