The frequency and/or intensity of extreme precipitation events and droughts is expected to increase in the Mediterranean basin for the XXI century. The Moroccan Middle-Atlas suffers from scarcity of observational hydrological data that are necessary for a coherent management of water resources. The precise study of the hydro-sedimentary dynamics of lakes can provide key information about past hydrological changes. We focused on the micro-scale analysis of well-dated sedimentary deposits of Lake Azigza (32°58’N, 5°26’W, 1,550 meters a.s.l.) in the Moroccan Middle-Atlas. A combined approach based on mineralogical and geochemical measurements coupled with microfacies characterization was conducted on the lacustrine sequences. We were able to provide proxies of runoff activity and lake level changes calibrated to regional hydro-climate or instrumental measurements available for the last 50 years. Past hydrological changes were then reconstructed for the last century at inter-annual to decadal time-scales. Our results highlight drastic lake level drops linked to variable regional precipitation regime and a marked change in the lake hydro-sedimentary dynamics since the last two decades. This recent change is unique regarding the last century.