Taforalt and El Harhoura 2, located on the Mediterranean and Atlantic coasts of Morocco, are two important Middle Stone Age (MSA) and Later Stone Age (LSA) archaeological sequences dating back >100 ka. In this research we developed a terrestrial palaeoaridity record for the Mediterranean and Atlantic coastal regions of Morocco using stable oxygen and carbon isotopes from Gerbillinae (gerbil) teeth to examine the impact of past climate change on human occupations and cultural behaviour in North Africa. Comparisons of the climate, environmental and cultural records from both sites show that during the intensive MIS 5 occupation periods, climate was relatively humid. However, MSA occupations of the sites are not exclusively associated with humid climate episodes, as several less ‘intense’ occupations occurred at the end of MIS 5, MIS 4 and MIS 3, periods associated with more arid conditions. The cultural transition from the MSA to the LSA occurs during MIS 2, a period of increased aridity across the western Mediterranean region, hinting that this cultural transition may be related to the changing environmental conditions. The oxygen and carbon isotope record shows that the coastal fringe of Morocco did not experience any marked periods of hyper-aridity during the Late Pleistocene, therefore suggesting that this region was a refugia for human populations.