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Glacier-fed streams are one of the environments most sensitive to global climate change. However, the effects of the freezing–thawing process on benthic macroinvertebrate communities in different habitats of glacier-fed streams are unclear. In this paper, we investigated benthic macroinvertebrates in riffles and pools of a glacier-fed stream in Xinjiang, China, during the pre-freezing period (November, 2018), freezing period (January 2019), and thawing period (April, 2019). Our results showed that the freezing–thawing process resulted in a decline in benthic macroinvertebrate species richness and diversity, both of which were attributed to the effects of the freezing–thawing process on habitat stability, water quality, and cycling of the stream ecosystems. During the whole freezing–thawing process, the indicator taxa of riffles were Rhithrogena sp. and Baetis sp., while the only indicator taxon of pools was Chironomus sp. The species richness, Margalef diversity, and EPT richness (Ephemeroptera, Plecoptera, and Trichoptera) of benthic macroinvertebrates in riffles were higher than those in pools, due to the higher habitat heterogeneity in the riffles. However, the density in riffles was significantly lower than that in pools during the freezing period (p &lt; 0.05). Additionally, pools were dominated by taxa with higher resilience and resistance traits, such as “bi- or multi-voltine”, “abundant occurrence in drift”, and “small size at maturity”. This result indicated that pools provide a temporary refuge for benthic macroinvertebrates in the extreme environment of glacier-fed streams. The freezing–thawing process plays an essential role in the formation of the structure and function of the stream ecosystem. Our results can help us to further understand the winter ecological process of headwater streams, and provide a reference for stream biodiversity conservation in cold regions.

The Impacts of the Freezing–Thawing Process on Benthic Macroinvertebrate Communities in Riffles and Pools: A Case Study of China’s Glacier-Fed Stream