Earth’s sand seas (dune fields) experience winds that blow with different strengths and from different directions in line with the seasons. In response, dune fields show a rich variety of shapes, from crescentic barchans to star and linear dunes. These dunes commonly exhibit complex and compound patterns with a range of length scales and various orientations, which up to now have remained difficult to relate to wind cycles. Here, we develop a model for dune orientation that explains the coexistence of bedforms with different alignments in multidirectional wind regimes. This model derives from subaqueous experiments, which show that a single bidirectional flow regime can lead to two different dune orientations depending on sediment availability, i.e., the erodibility of the bed. Sediment availability selects the overriding mechanism for the formation of dunes: increasing in height from the destabilization of a sand bed (with no restriction in sediment availability) or elongating in a finger on a non-erodible surface from a localized sand source. These mechanisms drive the dune orientation. Therefore, dune alignment maximizes dune orthogonality to sand fluxes in the bed instability mode, while dunes are aligned with the mean sand transport direction in the fingering mode. Applied to Earth’s deserts, the model quantitatively predicts the orientation of rectilinear dunes and their superimposed patterns. This field study suggests that many linear dunes on Earth elongate from sources, and are simply aligned with the mean sand transport direction.