Different upscaling methods for groundwater flow models are investigated. A suite of different upscaling methods is applied to several synthetic cases with structured and unstructured porous media. Although each of the methods applies best to one of the synthetic cases, no performance differences are formed if the methods were applied to a real three-dimensional case. Furthermore, we focus on boundary conditions, such as Dirichlet, Neumann, and Cauchy conditions, that characterize the interaction of groundwater with, for example, surface water and recharge. It follows that the inaccuracy of the flux exchange between boundary conditions on a fine scale and the hydraulic head on a coarse scale causes additional errors that are far more significant than the errors due to an incorrect upscaling of the heterogeneity itself. Whenever those errors were reduced, the upscaled model was improved by 70%. It thus follows that in practice, whenever we focus on predicting groundwater heads, it is more important to correctly upscale the boundary conditions than hydraulic transmissivity.