Aquatic ecosystems worldwide are deteriorating under the combined pressures of climate change, habitat fragmentation, and multi-source pollution. Conventional management has long relied on chemical water-quality metrics, yet these snapshots often fail to capture the biological integrity and functional health of entire watersheds.
In a new review published in Water & Ecology , a research team led by Jianfeng Peng from Tsinghua University and Dong Wang from Chinese Academy of Environmental Planning detailed how China’s 2022–2024 pilot program in the Yangtze River Basin is offering a broader perspective aquatic ecosystem health.
“The old paradigm asks whether the water is clean enough; the new question is whether the ecosystem itself is healthy and resilient,” say Peng and Wang. “That shift—from single-factor control to systemic governance—is what the Yangtze pilot is exploring through a more integrated framework for assessing ecological health.”
The pilot program established a unified yet differentiated assessment framework spanning 50 key water bodies and 331 monitoring sites. “Rather than applying uniform benchmarks across the basin, the pilot program applied distinct indicator sets for rivers, lakes, and reservoirs, selecting 14 secondary indicators from nearly 200 candidates,” share Peng and Wang. Target values were calibrated to relevant standards, regional ecology, and historical baselines, while current-status scores used three-year moving averages to smooth out hydrological variability. “This approach enabled what we called ‘one strategy for each lake and one strategy for each river’,” add Peng and Wang.
Notably, three years of implementation yielded roughly 20 000 field monitoring records and notable ecological gains. In the Chishui River Basin, decommissioning 342 small hydropower stations and removing 300 diversion dams restored natural connectivity, helping rare fish such as Spinibarbus sinensis to return. In the Dongting Lake Basin, converting intensive aquaculture ponds back to wetlands restored over 26 km² of aquatic vegetation, creating habitat for the critically endangered Emberiza aureola and numerous migratory birds. In Taihu Lake, aquatic vegetation coverage reached 200 km² in 2023, with annual increase of 25.8%, while algal bloom area and density dropped to their lowest levels since 2008.
Biological indicators showed observable recovery across the basin. Native fish species increased from 193 in 2022 to 230 in 2024. Compared with 2023, benthic organism species in the main stem rose by 11 to reach 107 in 2024. The Yangtze finless porpoise population climbed from 1 012 individuals in 2017 to 1 426 in 2025. Several species were recorded again after decades of absence: Coilia ectenes migrated upstream to the middle reaches for the first time in 30 years, and Anguilla japonica was recorded in the Chishui River for the first time in over 20 years.
The researchers identified three main practical lessons from the pilot. First, embedding ecosystem indicators into national management frameworks can encourage local authorities to address root stressors rather than isolated chemical parameters. Second, classification-based assessment proves useful in large, heterogeneous basins where natural geography and human pressures vary dramatically. Third, diverse restoration pathways, drawn from local diagnostic findings rather than prescribed templates, must be distilled into standardized, transferable protocols.
Looking ahead, the team calls for higher-resolution baseline surveys, a streamlined “retain-merge-replace-optimize” mechanism for the indicator matrix, and accelerated adoption of automated monitoring and multi-source data fusion, such as remote sensing, environmental DNA biomonitoring, and computational models, across the basin’s upper, middle, and lower reaches.
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Contact the author:
Jianfeng Peng
-Center for Water and Ecology, State Key Laboratory of Regional Environment and Sustainability, School of Environment, Tsinghua University, Beijing 100084, China
pengjf@tsinghua.edu.cn
Dong Wang
-United Center for Eco-Environment in Yangtze River Economic Belt, Chinese Academy of Environmental Planning, Beijing 100141, China
wangdong@caep.org.cn
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Water & Ecology
Systematic review
Not applicable
Monitoring and Assessment of Aquatic Ecosystems in the Yangtze River Basin
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.