Natural water level fluctuations (WLFs) are an inherent characteristic of Mediterranean inland waters, which are projected to be amplified by global climate change. La Caldera (Sierra Nevada National Park, Spain) is an oligotrophic high mountain lake (3050 m a.s.l.) that has experienced large fluctuations in water volume (13–100%) during the past 20 years due to irregular annual precipitation patterns (371–1816 mm). Because of the lake's cold and dilute abiotic environment, it is likely susceptible to projected increases in global temperature and represents an ideal sentinel of global change. We analyze the effect of WLFs on water quality and on plankton community in La Caldera to better understand the potential effects of recurrent droughts (3 droughts in a 20-year period) on lake ecology. We have found significantly positive effects of WLFs on total phosphorus (TP) concentrations. There was extreme variability in TP concentrations during three recurrent droughts (1995, 1999, and 2005) reflecting sediment resuspension. However, the data also suggest that this was not the only source of phosphorus. Extremely high P-enriched atmospheric dust inputs could have maintained the abnormally high TP in-lake concentrations measured during 2005. The data indicate that recurrent droughts have reduced lake resistance to TP changes but have increased lake resistance to total nitrogen (TN) changes, which supports the idea that a P-enriched atmospheric dust inputs during 2005. An increase in dissolved inorganic nitrogen (DIN)∶TP mass ratio after 2005 was observed, revealing a higher ecosystem homeostasis of this ratio.