The limited availability of high-resolution continuous archives, insufficient chronological control, and complex hydro-climatic forcing mechanisms lead to many uncertainties in palaeo-hydrological reconstructions for the Western Mediterranean. In this study we present a newly recovered 19.63 m long core from Lake Sidi Ali in the North African Middle Atlas, a transition zone of Atlantic, Western Mediterranean and Saharan air mass trajectories. With a multi-proxy approach based on magnetic susceptibility, carbonate and total organic C content: core-scanning and quantitative XRF, stable isotopes of ostracod shells, charcoal counts, Cedrus pollen abundance, and a first set of diatom data, we reconstruct Western Mediterranean hydro-climatic variability, seasonality and forcing mechanisms during the last 12,000 yr. A robust chronological model based on AMS C-14 dated pollen concentrates supports our high resolution multi-proxy study. Long-term trends reveal low lake levels at the end of the Younger Dryas, during the mid-Holocene interval 6.6 to 5.4 cal ka BP, and during the last 3000 years. In contrast, lake levels are mostly high during the Early and Mid-Holocene. The record also shows sub-millennial- to centennial-scale decreases in Western Mediterranean winter rain at 11.4, 10.3, 9.2, 8.2, 7.2, 6.6, 6.0, 5.4, 5.0, 4.4, 3.5, 2.9, 2.2, 1.9, 1.7, 1.5, 1.0, 0.7, and 0.2 cal ka BP. Early Holocene winter rain minima are in phase with cooling events and millennial-scale meltwater discharges in the sub-polar North Atlantic. Our proxy parameters do not show so far a clear impact of Saharan air masses on Mediterranean hydro-climate in North Africa. However, a significant hydro-climatic shift at the end of the African Humid Period (-5 ka) indicates a change in climate forcing mechanisms. The Late Holocene climate variability in the Middle Atlas features a multi-centennial-scale NAO-type pattern, with Atlantic cooling and Western Mediterranean winter rain maxima generally associated with solar minima.