Modelling of the land surface water-, energy-, and carbon balance provides insight into the behaviour of the Earth System, under current and future conditions. Currently, there exists a substantial variability between model outputs, for a range of model types, whereby differences between model input parameters could be an important reason. For large-scale land surface, hydrological, and crop models, soil hydraulic properties (SHP) are required as inputs, which are estimated from pedotransfer functions (PTFs). To analyse the functional sensitivity of widely used PTFs, the water fluxes for different scenarios using HYDRUS-1D was simulated and predictions compared. The results showed that using different PTFs causes substantial variability in predicted fluxes. In addition, an in-depth analysis of the soil SHPs and derived soil characteristics was performed to analyse why the SHPs estimated from the different PTFs cause the model to behave differently. The results obtained provide guidelines for the selection of PTFs in large scale models. The model performance in terms of numerical stability, time-integrated behaviour of cumulative fluxes, as well as instantaneous fluxes was evaluated, in order to compare the suitability of the PTFs. Based on this, the Rosetta, Wösten, and Tóth PTF seem to be the most robust PTFs for the Mualem van Genuchten SHPs and the PTF of Cosby et al. (1984) for the Brooks Corey functions. Based on our findings, we strongly recommend to harmonize the PTFs used in model inter-comparison studies to avoid artefacts originating from the choice of PTF rather from different model structures.