Detecting early warning signs of ecosystem degradation in nature reserves requires ultrasensitive biological indicators. We assessed the potential of using multihabitat assessment of benthic algae (growing on submerged vegetation, rocks, and dead trees) to detect early warning signs of nutrient enrichment in nine karstic lakes in Jiuzhaigou Nature Reserve, a World Natural Heritage site in China. Nonmetric multidimensional scaling analysis showed that variability in benthic diatom assemblages among the major habitats within lakes were generally higher than among lakes. Permutational multivariate analysis of variance indicated that epiphytic diatom assemblages dominated by Achnanthidium minutissimum (Kützing) Czarnecki differed significantly from both epilithic and epidendric assemblages. Epilithon and epidendron, both dominated by Delicata delicatula (Kützing) Krammer and Denticula tenuis Kützing, were not significantly different within lakes. Mean Bray–Curtis dissimilarity index values among the three assemblages in each lake were negatively correlated with the tourism-stress index but the correlation was not statistically significant. Increasing homogeneity in benthic diatom assemblages among habitats within a lake may be due to cumulative nutrient enrichment associated with tourism development. Links among tourisms, nutrient enrichment, and dissimilarity in benthic algae among habitats should be viewed with caution until the cause–effect relationships can be confirmed by in situ manipulative experiments.