The Chishui River is the prime production area for Jiang-flavor Baijiu in China, with 85% of the country's production capacity. To understand the spatial and temporal characteristics of fungal communities in the water column of the Maotai reach of the Chishui River and the relationship between fungal communities and environmental factors as well as the brewing of Jiang-flavor Baijiu, we analyzed the fungal species richness and diversity, structural changes, community composition, and correlation with environmental factors in different seasons and river reaches of the Chishui River Maotai reach. It was found that species richness and diversity followed the following seasonal pattern: summer >
autumn >
winter ≈ spring. Fungal species richness and diversity were significantly higher in polluted tributary river water than in main stream. The composition and structure of the fungal community varied in all seasons and in different river reaches. Ascomycota (76.5%), Basidiomycota (13.53%), and Chytridiomycota (9.37%) are the relatively dominant phyla, and a number of genera such as Trichosporon, Aspergillus, and Thermomyces have been reported to be associated with the brewing of Jiang-flavor Baijiu. In addition, total nitrogen (TN), chemical oxygen demand (COD), water temperature (WT), dissolved oxygen (DO), sulfate (SO