The evolution of the intermediate water masses within the southeastern corner of the Bay of Biscay is studied from the shelf edge and slope stations of a hydrographic standard section northward from Santander (43¿30'/43¿54'N, 3¿47'W). The section was sampled monthly from 1991 to autumn 2003 with some gaps more frequent in the early stages due to weather conditions. Data were systematically collected up to a 1000 m depth (or to the maximum depth at the shallower stations) showing a detailed picture of the variability in water masses below the mixing layer. Eastern North Atlantic Central Water has warmed as a consequence of continuous deepening of the isopycnal levels. Changes in water properties at fixed isopycnal levels are less relevant and highly biased by a 1998 positive peak in temperature and salinity. The warming trend found is 0.032¿C per year on average. On the other hand, the Mediterranean Water has been modified along isopycnals (variations 10 times greater than those due to isopycnal displacement) increasing progressively both temperature and salinity for the period 1994--2001. The values found are around 0.020¿C per year for temperature and 0.005 for salinity. As a final picture, all water masses below the mixing layer and down to a 1000 m depth in the southern Bay of Biscay have warmed up during the last decade at rates from two to six times greater than the those accepted for the North Atlantic during the last half century.