The paleoenvironmental changes recorded at the Khnifiss Lagoon, on the Saharan Atlantic coast, southern Morocco, during the last 3.5 kyrs BP puts another piece to the puzzle on the intricate relationship between North Atlantic climate patterns and climate variations in Northwest Africa. This study shed light on the hydroclimatic dynamics during a pivotal climatic period: the transition from the mid- to late Holocene and the termination of the African Humid Period. Our research unveils two key periods of salt marsh expansion at the Khnifiss Lagoon, approximately 3.5 and 2.7 kyrs BP when humidity conditions and increased marine influence were recorded. Those conditions paint a scenario of increased storminess and precipitation in NW Africa, compatible with a negative NAO-like climatic configuration. Our data revealed a synchronization between this scenario in NW Africa and cooling events in the North Atlantic during the transition from the mid-to-late Holocene, related to Rapid Climate Changes (RCCs) occurring between 3.5 and 2.5 kyrs BP, also known as the Bond event #2. These findings can potentially enhance climate prediction models, offering opportunities to better prepare for and adapt to the evolving climate patterns in the region. High-resolution paleoenvironmental records are still rare in Northwest Africa and are highly needed. The knowledge gained from these studies represents a critical step towards addressing the climate challenges in Northwest Africa and fortifying the region’s resilience in the face of climate change.