Oxygen depletion (temporal or permanent) in freshwater ecosystems is a widespread and globally important environmental problem. However, the factors behind increased hypolimnetic anoxia in lakes and reservoirs are often diverse and may involve processes at different spatial and temporal scales. Here, we evaluate the combined effects of different anthropogenic pressures on the oxygen dynamics and water chemistry of Lake Enol, an emblematic mountain lake in Picos de Europa National Park (NW Spain). A multidisciplinary study conducted over a period of four years (2013–2016) indicates that the extent and duration of hypolimnetic anoxia has increased dramatically in recent years. The extent and duration of hypolimnetic anoxia is typical of meso-eutrophic systems, in contrast with the internal productivity of the lake, which remains oligo-mesotrophic and phosphorus-limited. This apparent contradiction is ascribed to the combination of different external pressures in the catchment, which have increased the input of allochthonous organic matter in recent times through enhanced erosion and sediment transport. The most important among these pressures appears to be cattle grazing, which affects not only the import of carbon and nutrients, but also the lake microbiology. The contribution of clear-cutting, runoff channelling, and tourism is comparatively less significant. The cumulative effects of these local human impacts are not only affecting the lake metabolism, but also the import of sulfate, nitrate- and ammonium-nitrogen, and metals (Zn). However, these local factors alone cannot explain entirely the observed oxygen deficit. Climatic factors (e.g., warmer and drier spring and autumn seasons) are also reducing oxygen levels in deep waters through a longer and increasingly steep thermal stratification. Global warming may indirectly increase anoxia in many other mountain lakes in the near future.