Conflicting, even opposite interpretations on the evolution of the Southern Westerly Winds (SWW) are evident in paleoenvironmental records from southwestern Patagonia since the last ice age. These divergences call for new approaches utilizing different, ideally independent indicators of paleoenvironmental/paleoclimatic change from sensitive sites in climatically relevant locations. Here we present a multidecadally resolved diatom record from Lago Cipreses (51°S), a small closed-basin lake located in a bedrock depression along the eastern foothills of the southern Patagonian Andes. The hydrological balance evolution of this isolated lake affords a direct tie with SWW intensity in a mountainous sector where zonal wind strength and local precipitation are highly correlated. We detect cold-tolerant diatoms (small fragilarioids) between ∼14-11.9 cal. ka BP followed by a shift to planktonic assemblages (Discostella pseudostelligera, Aulacoseira spp.) under warmer Holocene conditions. Diatom assemblages indicative of stratified water-column conditions (Discostella pseudostelligera, Achnanthidium aff tepidaricola, Achnanthidium sieminskae) reached their maximum stability between ∼9.1-7.4 cal. ka BP. Stronger water-column mixing is evident by an abrupt species turnover to Aulacoseira spp. between ∼7.4-3.1 cal. ka BP, superimposed on centennial-scale alternations between assemblages since ∼6.1 cal. ka BP. Cold-tolerant diatoms resurge at ∼3.1 cal. ka BP and persist until the present. Our record offers assemblage-based evidence we interpret as sub-centennial to multimillennial scale changes in hydroclimate indicative of: (i) strong SWW influence between ∼14-11.9 cal. ka BP, (ii) a transition between ∼11.9-11.3 cal. ka BP to weak SWW influence between ∼11.3-6.5 cal. ka BP, with a SWW minimum between ∼9.1-7.4 cal. ka BP, and (iii) strong SWW influence since ∼6.5 cal. ka BP, with a Holocene SWW maximum since ∼3.1 cal. ka BP. We posit that enhanced hydroclimate variability since ∼6.1 cal. ka BP attests to the onset of Southern Annular Mode-like changes at centennial-to sub-centennial timescales. We detect a remarkably coherent and synchronous response of terrestrial and aquatic ecosystems at local scale since ∼14 cal. ka BP, highlighting the overriding importance of variations in SWW influence in terrestrial and aquatic environments at multiple timescales.