Abstract. High-altitude peat bogs and lacustrine records are very sensitive to climate changes and atmospheric dust input. Recent studies have shown a close relationship between regional climate aridity and enhanced eolian input to lake sediments. However, changes in regional-scale dust fluxes due to climate variability at short scales and how alpine environments were impacted by climatic- and human-induced environmental changes are not completely understood. Here we present a multi-proxy (palynological, geochemical and magnetic susceptibility) lake sediment record of climate variability in the Sierra Nevada (southeastern Iberian Peninsula) over the Holocene. Magnetic susceptibility and geochemical proxies obtained from the high mountain lake record of Laguna Hondera evidence humid conditions during the early Holocene, while a trend towards more arid conditions is recognized since ∼7000 cal yr BP, with enhanced Saharan eolian dust deposition until the present. This trend towards enhanced arid conditions was modulated by millennial-scale climate variability. Relative humid conditions occurred during the Iberian Roman Humid Period (2600–1450 cal yr BP) and predominantly arid conditions occurred during the Dark Ages and the Medieval Climate Anomaly (1450–650 cal yr BP). The Little Ice Age (650–150 cal yr BP) is characterized in the Laguna Hondera record by an increase in runoff and a minimum in eolian input. In addition, we further suggest that human impact in the area is noticed through the record of Olea cultivation, Pinus reforestation and Pb pollution during the Industrial Period (150 cal yr BP–present). Furthermore, we estimated that the correlation between Zr and Ca concentrations stands for Saharan dust input to the Sierra Nevada lake records. These assumptions support that present-day biochemical observations, pointing to eolian input as the main inorganic nutrient source for oligotrophic mountain lakes, are comparable to the past record of eolian supply to these high-altitude lakes.