Abstract: Renhuai City lies within the Chishui River Basin, a national-level nature reserve for rare and endemic fish species in the upper reaches of the Yangtze River. Moreover, it is the core production area for Maotai-flavor spirits in China. Understanding the health status of the rivers is conducive to the conservation of aquatic biological resources and the sustainable development of the society and economy in this area. We conducted a quarterly investigation of phytoplankton and environmental variables at 28 sampling sites along nine rivers in 2023. The relevant taxa were used as indicator organisms to evaluate the health status of these rivers. The results showed that: (1) A total of 96 species belonging to 52 genera and 7 phyla of phytoplankton were identified, which could be classified into 23 functional groups, among which 10 were dominant groups. (2) The seasonal succession tendency of functional groups was: S2/W1/Y (spring) → G/L-O-/W1/Y (summer) → S2/W1/Y (autumn) → S2 (winter). There were significant differences in the functional group composition between winter and summer as well as between the main stream of the Chishui River and its tributaries. Water pH, unclassified land use type (Uncla), total dissolved solids (TDS), and spatial factors (PCNM1, PCNM3, PCNM9, PCNM10) were the main environmental factors driving this ecological process. (3) Although the Q_r index (an ecological index based on functional groups) indicated that these rivers as a whole were in a “general-sub-healthy” state, the P-IBI (phytoplankton-integrated biotic index)  indicated a “sub-healthy-healthy” level. This study can provide basic data and technological support for the advancement of the Yangtze River comprehensive protection.

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