The shape of dunes depends on the history of wind regimes and sand availability. In deserts exposed to winds from two different directions but with comparable magnitude, dunes are found to be linear ridges, which are either perpendicular or parallel to the mean wind direction, depending on the angle between the two wind directions. These dunes, respectively observed for small and large angles between winds, are called transverse and longitudinal dunes. In both cases, their large width (hundreds of meters) and evolution time scale (years) strongly limit the investigation of their dynamics and thus our understanding of such structures. Here we show that, under water, similar structures can be obtained but at much smaller space and time scales. Performing controlled experiments together with numerical simulations, we highlight the physical mechanisms at play in the formation and long-term evolution of these structures. We show in particular that, while longitudinal dunes are stable and extend in time, transverse dunes are unstable. They evolve into wavy ridges and eventually break into barchans if the sand supply is too low. This fundamental difference is understood through the study of single sand piles and bars exposed to two winds. In the case of a large angle between winds, a sand pile grows a finger pointing in the average wind direction and transforms into a longitudinal dune. Such an elongation does not occur for a small angle where a sand pile evolves into a barchan. These results explain the morphological differences between straight and long longitudinal dunes and sinuous transverse dunes, while giving keys to infer the wind history or pattern state of development from the observation of dune shapes in the field.