Preferential flow at the Darcian scale may manifest as a consistent spatial pattern of high- and low-flow domains. The degree of persistence of these high- and low-flow domains with depth has important implications for the prediction of subsurface contaminant transport and the development of mitigation strategies to reduce pollution of sensitive environmental receptors. The objective of this study was to quantify the scale-dependent influence of a soil horizon interface on the vertical continuity of preferred flow domains. Spatial patterns of A and B horizon transient stream tube soil water flux were measured with vertical time domain reflectometry probes in a field soil under four different quasi-steady surface water application rates. The scale-dependent vertical continuity of stream tube soil water flux across the A–B horizon interface was quantified with Fourier-domain coherency spectra. Comparison of the A and B horizon fluxes across and within different water application rates revealed a loss of coherency between A and B horizon water flux with increasing flow rate between spatial scales of 1.0 to 6.75 and 0.38 to 0.50 m. The flux- and scale-dependent behavior of the horizon interface is probably the outcome of: (i) convergence of the pattern of preferred flow domains in the A horizon to the spatial pattern of the saturated hydraulic conductivity of the A horizon with increasing water application rate; and (ii) increased modification of the A horizon soil water flux pattern as the wetting front moves across the soil horizon interface. The results of this study indicate that the pedon, like the representative elementary volume, is hydrologically significant.