Fluorescent dye tracers are used to show concentration maps of tracer fronts, plumes and pathways on soil profiles and in monolith cross sections. The physical process of fluorescence from the exposed soil surfaces must be understood in order to retrieve accurately the concentration of such compounds. We found in a laboratory experiment that the fluorescence of quartz sand stained with Acid Yellow depends both on the tracer concentration and the soil water content. In this study, we investigate the dependence of fluorescence on the water content by using a radiative transfer model. The hypothesis of our modelling approach is that fluorescence depends on water content (1) because of the adsorption properties of the tracer and (2) because the microscopic distribution of the water phase changes the positioning and emission of the excited fluorescence molecules in the sample. Our model results show that both factors influence fluorescence to a similar extent, as observed in the Acid Yellow experiment. Because these results explain only part of the overall variation in the experiment, further factors, in addition to the postulated causes, have to be considered for determining concentration maps of fluorescent tracers from real soil profiles.