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Model conceptualisation is a key source of uncertainty in one-dimensional recharge modelling. The effects of different conceptualisations on transient recharge predictions for the semi-arid Uley South Basin, South Australia, were investigated. One-dimensional unsaturated zone modelling was used to quantify the effect of variations of (1) lithological complexity of the unsaturated zone, and (2) representation of preferential flow pathways. The simulations considered ranges of water-table depths, vegetation characteristics, and top soil thicknesses representative for the study area. Complex lithological profiles were more sensitive to the selected vegetation characteristics and water-table depth. Scenarios considering runoff infiltration into, and preferential flow through sinkholes resulted in higher and faster recharge rates. A comparison of modelled and field-based recharge estimates indicated that: (1) the model simulated plausible recharge rates, (2) only the models with preferential flow correctly reproduced the timing of recharge, and (3) preferential flow is probably redistributed in the unsaturated zone rather than passing to the water table directly. Because different but equally plausible conceptual models produce widely varying recharge rates, field-based recharge estimates are essential to constrain the modelling results.