Hydrological data collected in the Strait of Gibraltar have been used to examine the distribution and spatial–temporal evolution of the water masses in the area. The spatial variability has been addressed by means of a clustering method that determines the affinity of a collection of temperature–salinity samples to one of the water masses involved in the exchange. The method, which has been applied to a nearly-synoptic data set, highlights the clear evolution of the Mediterranean Waters as they flow westward through the Strait. While up to four different Mediterranean Waters are spatially distinguishable east of the main sill of Camarinal in the Strait, most of their differentiating characteristics are eroded after flowing over this restrictive topography due to mixing. West of the sill, therefore, speaking of a unique Mediterranean Water seems more appropriate. The same applies to the North Atlantic Central Water flowing in the opposite direction, which is noticeably modified along its path to the Mediterranean Sea, most of its transformation taking place in the Camarinal sill surroundings. A series of repeated transects carried out in the eastern and western sides of the Strait, provided a temporal analysis of the water masses evolution: the temporal variability manifests seasonality in the surface waters, while interannual signal is mainly detected in the deeper water masses. It is worth remarking the statistically significant positive trend of Western Mediterranean Deep Water (0.009 °C/year) and Winter Intermediate Water (0.03 °C/year), with the latter showing also intermittent occurrence in the Strait.