The objective of this study was to identify physical and chemical processes affecting Brilliant Blue (BB) transport in an unsaturated, macroscopically heterogeneous subsoil. We performed a BB leaching experiment in a 1-m-long undisturbed sandy monolith with a 10-cm-thick discontinuous clay layer 0.2 m below the surface. Two-dimensional BB concentration distributions were derived from image analysis at several depths in the monolith. Results showed several features of nonideal transport: (i) a deeper than expected travel depth, (ii) extensive tailing and a secondary peak in the BB depth profile, (iii) a lower than expected BB concentration in the upper part of the soil profile where the invading dye tracer solution was assumed to have replaced the initial solution, and (iv) a decrease in the concentration variability between the surface and the 2-cm depth. These results were in sharp contrast with inert transport experiments that suggested homogeneous flow and transport characterized by small dispersivity lengths. The macrostructure (i.e., the discontinuous clay layer and the nonuniform irrigation) determined the BB transport. A simulation with a one-dimensional transport model using an effective water content and sorption isotherm that was directly derived from the cross-sectional area of the clay layer suggested that the macrostructure alone was not sufficient to explain the BB distribution. Moreover, a two-site kinetic sorption model was needed to reproduce the tailing of the BB profile and the lower than expected concentrations at the soil surface. Since batch sorption experiments did not reveal rate-limited sorption, we postulate that the unsaturated flow conditions led to reduced accessibility of the sorption sites, thus decreasing the sorption rate.