Jiuzhaigou, characterized by its magnificent waterscapes and subalpine karstic features, is both a World Heritage Site and a World Biosphere Reserve in southwestern China. In recent years, this unique ecosystem has shown signs of stress due to increasing tourism activities within the reserve. The various routine methods, which monitor physical and chemical properties, do not fully reflect water quality in the subalpine and alpine lakes, while the indicators using aquatic organisms to evaluate the water quality or status of the subalpine lakes are poorly reported.