In the north-east Atlantic Ocean, the Bay of Biscay is an intersection between a coastal constrained dynamics (wide continental shelf and shelf break regions) and an eastern boundary circulation system. In this framework, the eddy kinetic energy is 1 order of magnitude lower than in western boundary systems. To explore this coastal complex system, a high-resolution (1 km, 100 vertical sigma layers) model experiment including tidal dynamics over a period of 10 years (2001–2010) has been implemented. The ability of the numerical environment to reproduce main patterns over interannual scales is demonstrated. Based on this experiment, the features of the (sub)mesoscale processes are described in the deep part of the region (i.e. abyssal plain and continental slope). A system with the development of mixed layer instabilities at the end of winter is highlighted. Beyond confirming an observed behaviour of seasonal (sub)mesoscale activity in other regions, the simulated period allows exploring the interannual variability of these structures. A relationship between the winter maximum of mixed layer depth and the intensity of (sub)mesoscale related activity (vertical velocity, relative vorticity) is revealed and can be explained by large-scale atmospheric forcings (e.g. the cold winter in 2005). The first submesoscale-permitting exploration of this 3-D coastal system shows the importance of (sub)mesoscale activity in this region with its evolution implying a potentially significant impact on vertical and horizontal mixing.