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A Quaternary stratigraphic stacking pattern on the Faro-Albufeira drift system has been determined by analysing a dense network of high-resolution single-channel seismic reflection profiles. In the northern sector of the system an upslope migrating depositional sequence (elongate separated mounded drift) parallel to the margin has been observed associated with a flanking boundary channel (Alvarez Cabral moat) that depicts the zone of Mediterranean Outflow Water (MOW) acceleration and/or focussing. A consequent erosion along the right hand border and deposition on the left hand flank is produced in this sector. The sheeted aggrading drift is the basinward prolongation of the elongate separated mounded drift, and developed where the MOW is more widely spread out. The overall sheeted contourite system is separated into two sectors due to the Diego Cao deep. This is a recent erosional deep that has steep erosional walls cut into Quaternary sediments. Two major high-order depositional sequences have been recognised in the Quaternary sedimentary record, Q-I and Q-II, composed of eight minor high-order depositional sequences (from A to H). The same trend in every major and minor depositional sequence is observed, especially in the elongate mounded drift within Q-II formed of: A) Transparent units at the base; B) Smooth, parallel reflectors of moderate-high amplitude units in the upper part; and C) An erosional continuous surface of high amplitude on the top of reflective units. This cyclicity in the acoustic response most likely represents cyclic lithological changes showing coarsening- upward sequences. A total of ten minor units has been distinguished within Q-II where the more representative facies in volume are always the more reflective and are prograding upslope with respect to the transparent ones. There is an important change in the overall architectural stacking of the mounded contourite deposits from a more aggrading depositional sequence (Q-I) to a clear progradational body (Q-II). We suggest that Q-I and Q-II constitute high-order depositional sequences related to a 3rd-order cycle at 800 ky separated by the most prominent sea-level fall at the Mid Pleistocene Revolution (MPR), 900–920 ky ago. In more detail the major high-order depositional sequences (from A to H) can be associated with asymmetric 4th-order climatic and sea-level cycles. In the middle slope, the contourite system has a syn-tectonic development with diapiric intrusions and the Guadalquivir Bank uplift. This syn-tectonic evolution affected the overall southern sheeted drift from the A to F depositional sequences, but G and H are not affected. These last two depositional sequences are less affected by these structures with an aggrading stacking pattern that overlaps the older depositional sequences of the Guadalquivir Bank uplift and diapiric intrusions.