AbstractIn this paper, we explore the secondary flows in the Danish Straits using observations and numerical simulations performed with the unstructured-grid hydrodynamic model SCHISM covering the North Sea and Baltic Sea. The straits are resolved on scales of up to 100 m. Given that large-scale atmospheric variability dominates the transport in these straits, we focus on the processes with subtidal time scales. Similarities and differences between the in- and outflows in the straits and flood and ebb flows in estuaries are analyzed. Contrary to the tidal straining in estuaries, the Danish Straits feature substantial differences in the stratification stability during the outflow and inflow phases. With a resolution of 100 m, new transport and mixing pathways that were previously unresolved appear fundamental to the strait dynamics. The variety of the strait morphology leads to high variability in the appearance of secondary circulation. Helical cells, often with a horizontal extension of 1 km, develop in the deep parts of the channels. A comparison between the high-resolution simulation and a simulation with a coarse grid of 500 m in the straits suggests that the coarser resolution overestimates the stratification and misrepresents the transport balance; the axial velocities and transport through the Sound are underestimated by 12%. These differences are explained by the missing secondary circulation when the coarse resolution is used (approximately two grid-points per cell instead of ten grid-points per cell in the fine resolution model), along with the resulting changes in mixing along the straits. In conclusion, the use of ultrafine resolution grids is essential to adequately resolve secondary flow patterns and two-layer exchange. Thus, the problems caused by the failure to resolve the secondary circulation in straits appear similar to the problems caused by the failure to resolve mesoscale eddies in ocean models.