Soil-atmosphere interaction has been attracting increasing interest as the seasonal variation of pore water pressures (pwp) has been linked to a variety of geotechnical problems (e.g. slope stability and serviceability, foundation subsidence or swelling, desiccation cracking etc.) or has been identified as part of the solution of geotechnical problems (e.g. in sustainable urban drainage systems). Prediction of how the pwp will change within soils of low permeability under the combined effect of evapotranspiration and precipitation requires adequate knowledge of the soil permeability and how it varies spatially (e.g with depth) and temporally (e.g. with suction or degree of saturation, void ratio or due to the opening and closing of desiccation cracks). Nonetheless, in-situ measurements of permeability that satisfy both the spatial and temporal variation are difficult. In order to clarify the importance of variable permeability in predicting pwp variations under atmospheric loads, a series of one- and two-dimensional finite element analyses was performed, where the permeability model and the variation of permeability were parametrically studied. The results demonstrated that the variation of permeability, as well as the model employed in the analysis, e.g. allowing or not for desiccation cracking, influenced the values of suction calculated as well as the pwp profile with depth, highlighting the importance of estimating the spatial and temporal variation of permeability with some level of confidence.