Wind- and water-driven migrating sand dunes frequently interact with elevated natural and manmade topographical features. The dune-obstacle interaction can alter the migrating behaviour of the dune and, depending on the nature of the obstacle, it may generate various societal and technological risks. Here we study the problem of dune-obstacle interaction in a paradigmatic quasi-2D domain realised in a subaqueous laboratory experiment. Generically, dunes interact with obstacles either by ‘crossing’ over the obstacle or by being ‘trapped’. We describe how the selection of these two distinct dynamical behaviours depends on the size and shape of the obstacle, focusing in particular on the fluid flow in the immediate vicinity of the obstacle. Specifically, we perform a modal decomposition of the measured flow field and we discover that the outcome of the dune-obstacle interaction is closely related to the flow structure above the obstacle.