Dune fields often show abrupt changes in morphology over short distances, but the mechanism driving the changes has been unclear. Physical modelling and airborne altimetry from White Sands, New Mexico, show that the development of an internal boundary layer is linked to the vegetation and hydrologic patterns observed there. Desert dunes often exhibit remarkable changes in their morphology over short distances. For example, sediment-rich dunes can break up into smaller, isolated features, and then become stabilized by plants, over distances of kilometres1,2,3,4,5,6. These pattern transitions often coincide with spatial variations in sediment supply1,3,5, transport rate6,7, hydrology8 and vegetation9,10,11, but these factors have not been linked mechanistically. Here we hypothesize that the abrupt increase in roughness at the upwind margins of dune fields triggers the development of an internal boundary layer12,13,14,15,16,17,18 that thickens downwind and causes a spatial decrease in the surface wind stress. We demonstrate that this mechanism forces a downwind decline in sand flux at White Sands, New Mexico, using a combination of physical theory14,15,16,17,18,19, repeated airborne altimetry surveys and field observations. The declining sand flux triggers an abrupt increase in vegetation density, which in turn leads to changes in groundwater depth and salinity—showing that aerodynamics, sediment transport and ecohydrology are tightly interconnected in this landscape. We conclude that, despite the documented complex climatic and geologic history of White Sands20, internal boundary layer theory explains many of the observed first-order patterns of the dune field.