Groundwater modelling was conducted to support an application for wastewater disposal into deep saline aquifers at an oil and gas facility. The risk of wastewater migration from the injection points up to shallow aquifers and surface was quantified and shown to be acceptably low. A confined multi-layer FEFLOW model was constructed to simulate the deep aquifer system in isolation. A historical dataset of water injection into the system was available, so a highly parameterized calibration approach was used in conjunction with nonlinear uncertainty analysis. Further assessments required the use of the Sandia Waste-Isolation Flow and Transport (SWIFT) model. Therefore, custom software was developed to facilitate the conversion from FEFLOW to a SWIFT model. By applying the multiple alternative parameter sets produced by the nonlinear uncertainty analysis to the predictive model, the risk of adverse wastewater migration could be assessed.