This paper presents Early to Late-Holocene sedimentary deposits from the Moulouya catchment, the main Mediterranean river basin of Morocco. Within this region, recent studies have focused particularly on marine or lacustrine archives. Studies on fluvial archives are thus important for improving our understanding of palaeoenvironmental responses to Holocene climatic changes at regional and supra-regional scales. Here, we studied alluvial archives from two basins 300 km apart in the mid-Moulouya basin and High Plateaus region located in the rarely studied NW African highlands, which are currently defined by arid and cold climatic conditions. Strong similarities between these deposits in terms of morpho-pedosedimentary and chronostratigraphical evolution demonstrate a regional morphogenic pattern controlled by Holocene climatic changes. Using a multi-proxy approach, we document rapid palaeoenvironmental changes and orbital-scale morphogenic changes. Four particular phases of regional geomorphic stability have been dated to ca. 10800–10500, 10200–9900, 9300, and 8900 cal. BP. Enhanced flooding periods that reflect times of climatic aridification may correlate with Early and Mid-Holocene Rapid Climatic Changes, especially during the 9.2 ka event. Furthermore, the Moulouya alluvial archives record the development of an extensive wetland formation and tufa sedimentation within the alluvial plains between ca. 10.8 to 6-5 cal ka BP. This formation is recognised at a regional scale across the upper and mid-Moulouya catchments, whereas it is missing from other Moroccan fluvial archives. These lasting humid climatic conditions (ca. 10.8–6/5 ka cal. BP.) are consistent with those recorded in the sub-Saharan records during the last African Humid Period (AHP), and suggest a potential linkage between the NW African highlands and the Saharan domain. Hence, we assume that this fluvio-palustrine wetland formation located at 32°–34°N is consistent with the northern archives recording AHP wet conditions.