Hygrothermal models are important tools for assessing the risk of moisture-related decay mechanisms which can compromise structural integrity, loss of architectural features and material. There are several sources of uncertainty when modelling masonry, related to material properties, boundary conditions, quality of construction and two-dimensional interactions between mortar and unit. This paper examines the uncertainty at the mortar-unit interface with imperfections such as hairline cracks or imperfect contact conditions. These imperfections will alter the rate of liquid transport into and out of the wall and impede the liquid transport between mortar and masonry unit. This means that the effective liquid transport of the wall system will be different then if only properties of the bulk material were modelled. A detailed methodology for modelling this interface as a fracture is presented including definition of material properties for the fracture. The modelling methodology considers the combined effect of both the interface resistance across the mortar-unit interface and increase liquid transport in parallel to the interface, and is generalisable to various combinations of materials, geometries and fracture apertures. Two-dimensional DELPHIN models of a clay brick/cement-mortar masonry wall were created to simulate this interaction. The models were exposed to different boundary conditions to simulate wetting, drying and natural cyclic weather conditions. The results of these simulations were compared to a baseline model where the fracture model was not included. The presence of fractures increased the rate of absorption in the wetting phase and an increased rate of desorption in the drying phase. Under cyclic conditions, the result was higher peak moisture contents after rain events compared to baseline and lower moisture contents after long periods of drying. This demonstrated that detailed modelling of imperfections at the mortar-unit interface can have a definitive influence on results and conclusions from hygrothermal simulations.