Cold-water corals (CWCs) are widely distributed in the entire Alboran Sea (western Mediterranean Sea), but only along the Moroccan margin they have formed numerous coral mounds, which are constrained to the West and the East Melilla CWC mound provinces (WMCP and EMCP). While information already exists about the most recent development of the coral mounds in the EMCP, the temporal evolution of the mounds in the WMCP was unknown up to the present. In this study, we present for the first time CWC ages obtained from four sediment cores collected from different mounds of the WMCP, which allowed to decipher their development since the last deglaciation. Our results revealed two pronounced periods of coral mound formation. The average mound aggradation rates were of 75–176 cm kyr−1 during the Bølling-Allerød interstadial and the Early Holocene, only temporarily interrupted during the Younger Dryas, when aggradation rates decreased to <45 cm kyr−1. Since the Mid Holocene, mound formation significantly slowed-down and finally stagnated until today. No living CWCs thrive at present on the mounds and some mounds became even buried. The observed temporal pattern in mound formation coincides with distinct palaeoceanographic changes that significantly influenced the local environment. Within the Alboran Sea, enhanced surface ocean productivity and seabed hydrodynamics prevailed during the Bølling-Allerød and the Early Holocene. Only with the onset of the Mid Holocene, the area turned into an oligotrophic setting. The strong hydrodynamics during the mound formation periods are most likely caused by internal waves that developed along the water mass interface between the Modified Atlantic Water and the Levantine Intermediate Water. In analogue to observations from modern CWC settings, we assume that internal waves created turbulent hydrodynamic conditions that increased the lateral delivery of particulate material, promoting the availability of food for the sessile CWCs. Overall, our data point to the dominant role of the water column structure in controlling the proliferation of CWCs and hence the development of coral mounds in the southern Alboran Sea.