Mountain lakes are particularly fragile ecosystems undergoing important transformations associated with ongoing global change. However, the history of anthropogenic impacts on mountain lakes and their catchments is much longer, in many cases featuring millennia of summer pastoral farming. More recently, the growing demand for raw materials and energy linked to industrialization, particularly accelerated since the 19th century CE, meant a further increase in human impact on mountain areas. The Cantabrian Range (northern Spain) constitutes a paradigmatic case of southern European mountain range experiencing intense human impact during the past few millennia and particularly the past two centuries. Here, we have reconstructed the environmental dynamics of this area during the last millennium, with a particular focus on the impact of mining, based on the multidisciplinary analysis (sedimentology, biogeochemistry, magnetic susceptibility, diatoms, pollen, charcoal and dung fungal spores) of sediment cores from Lago de La Cueva (43°03′N, 6°06′W, 1550 m a.s.l.). Changing land use and climate have driven lake dynamics during the last centuries. A major fire-caused deforestation event dated to the late 15th century CE increased erosion and the frequency of intense runoff episodes, in the context of the wetter and colder Little Ice Age. The onset of iron mining activities in the catchment ca. 200 years ago had a strong impact on the lake. Sedimentation rates notably raised and mining waste containing hematite and potentially toxic elements (e.g. Fe, Co, As) was washed into the lake. Additionally, diatom assemblages showed that lake regulation since the early 20th century CE severely altered the natural hydrological regime introducing rapid seasonal lake-level oscillations and increased lakeshore erosion, water turbidity and nutrient loads. The recent environmental restoration, finished in 2006, has involved the re-deposition of large volumes of mine tailing. Although some mining wastewater still arrives into the lake because mine drainage is still active, restoration works have succeeded in reducing erosion rates and nutrient loads. Lower land-use intensity has also contributed to natural vegetation recovery, further diminishing erosion. This study illustrates the complex interactions between human activities (grazing, mining, hydropower) and climate change in defining mountain landscape shifts through time. Moreover, our results highlight the usefulness of paleolimnological research to quantitatively assess the effectiveness of lake restoration programs.