Pipe structures are commonly encountered in the geophysical context, and in particular in sedimentary basins, where they are associated with fluid migration structures. We investigate pipe formation through laboratory experiments by injecting water locally at a constant flow rate at the base of water-saturated sands in a Hele–Shaw cell (30 cm high, 35 cm wide, gap 2.3 mm). The originality of this work is to quantify the effect of a discontinuity. More precisely, bilayered structures are considered, where a layer of fine grains overlaps a layer of coarser grains. Different invasion structures are reported, with fluidization of the bilayered sediment over its whole height or over the finer grains only. The height and area of the region affected by the fluidization display a non-monotonous evolution, which can be interpreted in terms of fluid focusing vs. scattering. Theoretical considerations can predict the critical coarse grains height for the invasion pattern transition, as well as the maximum topography at the sediment free surface in the regime in which only the overlapping finer grains fluidize. These results have crucial geophysical implications, as they demonstrate that invasion patterns and pipe formation dynamics may control the fluid expulsion extent and localization at the seafloor.