The southern Bay of Biscay (NW Spain) shows a very active hydrography due to the different origins of its Central Waters, the local modifications exerted on them by continental effects and the recurrence of mesoscale processes such as slope currents, upwellings and eddies. In order to assess the role of the different sources of variability we conducted a monthly series of CTD sampling in the central Cantabrian Sea along a coastal-oceanic transect, from 1993 to 2003. We analyzed the spatial variability of the hydrographic processes over different timescales. The thermohaline properties of Central Waters varied between those typical of the subpolar mode of the Eastern North Atlantic Central Water (ENACWsp) and a local mode, the Bay of Biscay Central Water (BBCW), though there has been a clear shift toward the BBCW prevalence in the last years. The Iberian Poleward Current (IPC) conveyed subtropical Central Waters (ENACWst) into the region almost every winter. This slope current may display a double-core structure during some extreme events. The upper layers of the ocean showed a long-term trend toward increasing temperature and decreasing salinity, and accordingly density was on the decrease. These patterns suggest an enhancement of the water column stratification. Coastal upwellings are an important source of inshore variability and counteract these long-term changes on the coast. However, their intensity seems to be decreasing and their seasonal pattern changing toward a general advancement of the upwelling-favorable season.