The transferability of soil hydraulic properties measured in the laboratory to the field or catchment scale is a key problem in soil hydrology. To narrow the gap between laboratory and field scale we investigated soil water movement at the lysimeter scale. Specific questions of interest are the existence and uniqueness of effective hydraulic properties for lysimeters that are internally heterogeneous. To answer these questions, synthetic measurements of water contents, pressure heads, and fluxes across the system boundaries were generated by forward modelling of water flow, based on the Richards equation, for a variety of homogeneous and layered soils and under varying types of boundary conditions (multistep outflow, evaporation, transient atmospheric). We evaluated the measurements by inverse modelling assuming a homogeneous system. The globally convergent shuffled complex evolution algorithm was applied to avoid parameter estimation problems caused by a rough topology of the objective function. The hydraulic properties of homogeneous soils were always uniquely identified, not only for the classic multistep outflow and evaporation experiments but also under natural atmospheric boundary conditions. Moreover, for the weakly heterogeneous layered soils, the soil water dynamics could be well described with effective homogeneous properties. For highly heterogeneous, layered soils, it was still possible to match the boundary fluxes for all types of experiments. Internal system states could not be matched, however, and the properties identified depended on the type of experiment. For these soils no unique effective soil hydraulic properties exist. We found that for strongly layered soils the simultaneous determination of the hydraulic properties of multiple soil layers by inverse modelling is a practicable alternative to the description with effective parameters.