Hygrothermal models are important tool for assessing the risk of moisture-related decay mechanisms such as freeze-thaw in historic masonry structures. There are several sources of uncertainty when modelling masonry, related to material properties, boundary conditions, quality of construction and twodimensional interactions between mortar and unit. This paper examines one potential source of uncertainty; the imperfect nature of mortar joints. This interface may feature hairline cracks or imperfect bonds which can be modelled as a fracture. This 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 measured properties of the bulk material were modelled. A detailed methodology for modelling the interface as a fracture is presented including material property definition. Two-dimensional DELPHIN models of masonry walls were created to simulate this interaction with varying levels of fracture widths (apertures). A series of hygrothermal simulations were performed to demonstrate change in moisture profile from the baseline condition. A significant increase in moisture absorption was found. This was dependent on aperture size, material and the relative size of the masonry modelled.