The long-term storage of nuclear waste is an engineering challenge being investigated around the world. The Canadian deep geological repository (DGR) design consists of a multiple barrier system including a used fuel container (UFC) surrounded by bentonite within a low permeability host rock. The bentonite buffer that surrounds the UFC is designed to limit the ingress of chemical species towards the UFC and minimize egress of radionuclides away from the UFC. In addition, the UFC consists of an inner steel container that resists the expected pressures at 500-800 m below the ground surface and is coated in copper which acts as a barrier against corrosion. Sulphide that is remotely produced by sulphate reducing bacteria far away from the UFC, can diffuse through the bentonite buffer and result in UFC corrosion. Modelling the transport of sulphide is therefore critical to determining the expected corrosion on the surface of the UFC. Accordingly, a three dimensional (3D) finite element model of the Canadian DGR was developed with emphasis on capturing the unique 3D UFC geometry and expected repository layout. The numerical model was implemented using COMSOL Multiphysics, and sulphide diffusion through the buffer was simulated using Fick’s Law incorporating a temperature dependent diffusion coefficient. The temperature in the DGR is expected to peak close to 100°C in the first 100 years due to the thermal radiation of heat from the used nuclear fuel. The results show an interesting variation of sulphide transport throughout the DGR indicating the benefits of 3D modelling. In addition, diffusion coefficients increase by a factor of 4 compared to background levels with temperatures near 100°C and lead to a sulphide flux increase in the DGR. The model includes diffusion coefficients that change spatially and temporally to fully capture the effect on sulphide flux.