In this study, we have attempted to determine the effective hydraulic properties of a highly heterogeneous soil horizon composed of two elementary pedological volumes (EPVs). Our upscaling approach was guided by the “scaleway” approach, in which the properties of a complex system can be estimated by multiple discrete upscaling steps. This approach was tested on a data set from laboratory measurements of hydraulic conductivity at the EPV scale, while an explicit three-dimensional soil structure was considered at the horizon scale. We then formulated a decision tree to guide the choice of the appropriate upscaling method to determine the effective hydraulic conductivity at the horizon scale. In the case of low contrast between hydraulic conductivities at the EPV scale, the effective hydraulic conductivity at the horizon scale can be achieved by calculating the Wiener bounds, which requires only the proportion of the different EPVs. In the case of high contrast between hydraulic conductivities at the EPV scale, we recommend either calculating the Cardwell and Parson bounds, or performing a direct three-dimensional numerical simulation to solve Richards' equation, which requires an explicit representation of the three-dimensional structure of the soil horizon. The Cardwell and Parsons bounds remains a good and easily available approximation. Otherwise, more accurate estimation can be obtained by numerical simulation, although this is time consuming. A decision map is proposed to help choose the best method to estimate the effective hydraulic conductivity.