A common approach for simulating dewatering/transport problems in mining and tunnelling engineering is to use a regionally calibrated groundwater model. MODFLOW’s unstructured grid (USG) is a recent advancement that can allow the creation of unstructured grid to facilitate local refinement modelling groundwater problems such as these. Transferring the calibrated model boundaries from the regional mesh to the local refined grids with USG approach can result inconsistencies in the water budget and the mass balance. In this paper, the impact on water budget as a result of variation of grid, grid size and numerical approaches (upscaling, ghost node correction) is analysed. The examination in a local dewatering design showed that high uncertainty occurs if model boundaries are not transformed and assigned correctly. The paper further outlines effective methods to transfer a variety of model boundaries from larger scale regional groundwater model to local, refined grid model such that numerical uncertainties can be reduced.