In designing climate exposed soil structures such as caps and covers over mine waste it is necessary to include the wetting and drying influences of the local climate in order to accurately predict the net water, vapour and oxygen fluxes across the ground surface and through the base of the covers. The most advanced evaporative flux modelling tools currently available to practitioners have been limited to rigorous one-dimensional models (ie SoilCover) or semi-empirical two-dimensional models (ie Hydrus-2D). It is common practice to use the rigorous one-dimensional evaporative flux model results to develop a surface boundary function that can then be applied within a saturated/unsaturated two-dimensional model. However, this is not an ideal situation and results in a further approximation of the real system being modelled. This paper will highlight the use of a new modelling tool, VADOSE/W, which brings existing, rigorously formulated evaporative flux theory into the familiar setting of a two-dimensional model. The model is enhanced for simultaneous two-dimensional oxygen gas transport analysis, which has direct application in the mine waste industry. A key focus of the paper will be addressing the limitations of one-dimensional analysis for cover systems on sloping and hummocky terrain.