Assessment of the Ecological Status of the Yangtze River Based on Water Quality, Phytoplankton, and Periphyton

The Yangtze, Asia’s longest river, supports ecosystems and people, but rising stress from development is degrading water quality and altering algae. Using 2016–2021 water quality data from 83 sites and 2021 phytoplankton (55 sites) and periphyton (44 sites) surveys, this study analyzes the spatiotemporal variations in water quality and algal communities in the Yangtze River mainstream and the driving mechanisms via Mann–Kendall trends, random forest modeling, and hierarchical partitioning. The results revealed significant long-term declines in TN, TP, ammonia nitrogen, and permanganate indices, with a rising water quality index (WQI), reflecting effective basin-wide pollution control. Spatially, the Jinsha River segment maintains a high WQI and low nutrient content, whereas the downstream reaches present increasing TN, TP, and ammonia nitrogen along the longitudinal gradient in 2021, reflecting the cumulative effects of intensified anthropogenic activities from the headwaters to the estuary. Phytoplankton density increases downstream and is correlated with nutrient enrichment, with cyanobacteria/Chlorophyta dominance in the middle–lower reaches. The periphyton density peaks in the middle reaches (1.76 × 108 cells/cm2), which is driven by the optimal temperature, nutrients, and substrates. Integrated ecological assessment via random forest models classified 85% of the sites as “good” or “excellent,” but 15% of the lower-reach sites were rated “moderate,” highlighting nutrient-induced ecological stress. Mantel tests and hierarchical partitioning identified TN as the primary driver of phytoplankton community composition, whereas water temperature emerged as the key factor shaping periphyton distribution. These findings underscore the necessity of differentiated management strategies: strict conservation of upstream pristine habitats and enhanced nitrogen–phosphorus control in downstream industrialized zones.