The phytohormone auxin is implied in steering various developmental decisions during plantmorphogenesis in a concentration-dependent manner. Auxin maxima have been shown to maintainmeristematic activity, for example of the root apical meristem, and position new sites of outgrowth, suchas during lateral root initiation and phyllotaxis. More recently, it has been demonstrated that sites ofauxin minima also provide positional information. In the developing Arabidopsis fruit, auxin minima arerequired for correct differentiation of the valve margin. It remains unclear, however, how this auxinminimum is generated and maintained. Here we employ a systems biology approach to model auxintransport based on experimental observations. This allows us to determine the minimal requirements forits establishment. Our simulations reveal that two alternative processes — which we coin “flux-barrier”and “flux-passage” — are both able to generate an auxin minimum, but under different parametersettings. Both models are in principle able to yield similar auxin profiles but present qualitatively distinctpatterns of auxin flux. The models were tested by tissue-specific inducible ablation, revealing that theauxin minimum in the fruit is most likely generated by a flux-passage process. Model predictions werefurther supported through 3D PIN-localisation imaging and implementing experimentally observedtransporter localisation. Through such an experimental-modelling cycle, we predict how the auxinminimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal.