Alpine lakes are usually unaffected by anthropogenic disturbance, yet these aquatic ecosystems are highly sensitive to climate warming and atmospheric deposition. It is unclear how water quality of alpine lakes has responded to these environmental changes. Unprecedented degradation in water quality (characterized by nutrient enrichment and phytoplankton blooms) had occurred in the Tianchi Lake, an alpine lake in the Tianshan Mountains. Here we measured the dust and precipitation chemistry to assess the source, magnitude, and impact of atmospheric deposition on nutrient stoichiometry of Tianchi Lake. Long-term (2015–2021) limnological data consisted of nutrient and chlorophyll were used to quantify the trends of lake water quality, as well as the association between phytoplankton biomass and air temperature. We proposed a critical nutrient model based on water quality guarantee probability to estimate the maximum allowable nutrient load. The results indicated that air pollutants from urban agglomeration and dust derived from semi-arid region represented the primary sources of atmospheric nutrient, which contributed 6.86 t nitrogen (N) and 0.23 t phosphorus (P) to the lake during 2021. Enhanced fertilization effect on phytoplankton due to high atmospheric deposition was expected to promote phytoplankton blooms, but unbalanced N:P ratio would exacerbate the P limitation of primary productivity. Climate warming seemed equally crucial synergistically to stimulate phytoplankton growth, the first appearance of phytoplankton blooms corresponded to the beginning of the warm period. Further studies had shown that increase in frequency and duration of heat waves would accelerate the eutrophication. To mitigate water quality degradation, the critical nutrient model suggested that 40.63 t N and 0.49 t P should be reduced. We conclude that the synergistic effects of climate warming and atmospheric deposition exacerbate the water quality of Tianchi Lake, even though it was protected well by strict environmental policies. More studies should be conducted to assess the potential impact of climate warming and atmospheric deposition on alpine lakes to ensure water quality safety and water ecological security. © 2023 The Authors