Soils often exhibit a variety of small-scale heterogeneities such as inter-aggregate pores and voids which partition flow into separate regions. In this paper a methodological approach is discussed for characterizing the hydrological behaviour of a heterogeneous clayey-sandy soil in the presence of structural inter-aggregate pores. For the clay soil examined, it was demonstrated that, coupling the transfer function approach for analyzing BTCs and water retention data obtained with different methods from laboratory studies captures the bimodal geometry of the porous system along with the related existence of fast and slow flow paths. To be effectively and reliably applied this approach requires that the predominant effects of the soil hydrological behaviour near saturation be supported by accurate experimental data of both breakthrough curves (BTCs) and hydraulic functions for high water content values. This would allow the separation of flow phases and hence accurate identification of the processes and related parameters.