A key difficulty in air pollution dispersion modelling and quantifying area-fugitive emission fluxes of pollutants from open-pit mines is that the meteorological fields for such complex terrains cannot be reliably predicted using simplistic surface layer theory. This has fueled research in the Computational Fluid Dynamics (CFD) approach to predict the atmospheric transport phenomena for such terrains more accurately. In this study, transport phenomena over a shallow (100 m) and a deep (500 m) synthetic mine are predicted under thermally unstable, neutral, and stable conditions using CFD. The skimming flow, which is characteristic of flow over cavities with a separation of flow inside the cavity from the ambient flow outside, is only predicted under the thermally neutral case, while more complex flow patterns emerge otherwise. Under the thermally unstable case, the shallow and deep mines induce enhanced mixing of flow downstream of the mine, resulting in substantial plume rise and dilution of the pollutants released from the mine. Under the thermally stable case, the plume from the shallow mine is restricted to the surface layer downstream of the mine. However, under the thermally stable case, the plume from the deep mine rises into the substantial portion of the boundary layer due to the formation of a standing wave over and inside the mine. The results suggest that the CFD model can predict transport phenomena over open-pit mines reliably so that the meteorological fields may be ingested in operational air quality and emission flux models to improve the accuracy of their predictions.