The present study addresses the analysis of changes in marine primary productivity derived from climatic variability over the last 30,000 yr. The study area is the Alboran Sea; this is the westernmost basin of the Mediterranean Sea, and was a very sensitive area to changes in sea levels and atmospheric configuration during the last glacial–interglacial transition. We report the results from four sediment cores recovered in both the western and eastern Alboran basins. This allowed us to monitor the W–E evolution of the hydrological structures. The study is mainly based on the diatom record, although total organic carbon (TOC), isotopes and UK′37-SST were also used to gain further information. Paleoceanographic conditions favoured high paleoproductivity rates during the Last Glacial Maximum, although this occurred at Termination 1a and during the Younger Dryas event (YD), increasing towards the easternmost sites. During these periods, meteorological conditions, with increased westerlies, intensified the flow to the east, driving an eastward migration of the Western Anticyclonic Gyre. A possible displacement of the North Alboran upwelling system is also considered. The major component of the diatom assemblage during the YD are the resting spores of Leptocylindrus danicus, which suggest the presence of cooler and less saline surface waters. The opposite behaviour between planktonic and benthic proxies in addition to the high TOC values allows us to infer a phase of reduced deep water renewal between 16.5 and 9 cal ky BP. Fresh-water diatoms and opal phytoliths were used as indicators of aridity and humid land-conditions, respectively. During the glacial period and until 14 cal ky BP we observed a gradual climatic deterioration, accompanied by a loss of grass belts. Climatic conditions were warmer and moister during the Bølling–Allerød while the YD was dry. The re-establishment of vegetation belts and replenishment of lakes was observed at 8 cal ky BP.