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. Thus, in this study, benthic diatoms from multiple habitats in Jiuzhaigou were sampled and assessed for water quality monitoring. Canonical Correspondence Analysis(CCA) showed that the canonical coefficients for elevation, water temperature and total nitrogen on the first Canonical Correspondence Analysis axis were-0.84, 0.78 and-0.53, respectively, environmental variables associated with the distribution patterns of benthic diatoms. The dominance of diatom taxa indicative of nutrient enrichment indicates a clear trend toward eutrophication in the Pearl Shoal and Colorful Lake, two of the sites mostly visited by tourists. It was observed that the effect of the type of substratum on diatom community composition is not significant in subalpine lakes. The most dominant species in Jiuzhaigou lakes are the genera Achnanthes, Fragilaria, Cymbella, Cocconeis, Diatoma and Denticula. In combination with dominant and sensitive species in the benthic diatom communities, CCA and CA methods can be used to evaluate the impact of human activities on subalpine karstic lakes. The dominance of diatom taxa is indicative of nutrient enrichment and the results of CCA and CA indicate a clear trend toward eutrophication in the Pearl Shoal and Colorful Lake, two of the sites mostly visited by tourists.
