Since 2017, a fishing ban in the Chishui River (China) has reduced human disturbances, yet the early-stage recovery of fish resources remains unquantified. Here, we applied environmental DNA (eDNA) metabarcoding to assess fish diversity and restoration status across its upper, middle, and lower reaches. An analysis of operational taxonomic units (OTUs) revealed higher unique than shared OTUs among reaches, indicating significant spatial partitioning of fish communities. The upper reaches exhibited the highest diversity due to reduced human activity, attributed to greater species richness, while the middle and lower reaches showed similar community structures. Key findings include the following: (1) the detection of rare endemic species (Schizothorax) and non-native Oreochromis DNA, suggesting invasion risks; (2) the investigation revealed a predominance of small-bodied fish species, indicating that large-bodied fish populations in the Chishui River (China) remained relatively scarce; (3) the recovery of demersal fish DNA from surface waters, confirming eDNA’s broad detection capacity. The results indicate that the fishing ban has contributed to the partial recovery of the fish community in the Chishui River (China). However, risks of biological invasion (e.g., Oreochromis species) remain, and large-bodied fish are still relatively scarce. To ensure effective conservation, it is critical to strengthen the monitoring and evaluation of the fishing ban’s effectiveness and implement timely measures to prevent invasive species proliferation.

Urbanization-driven land use transitions, especially impervious surface expansion, profoundly affect aquatic ecosystems, yet the regulatory mechanisms of microbial assembly and disassembly remain unclear. Using environmental DNA metabarcoding, this study examined relationships between landscape patterns, environmental gradients, and microbial communities in the middle-lower Yangtze River. Impervious surfaces (source landscapes) increased from 10% (midstream) to 37% (downstream), disrupting source–sink balance, elevating nitrogen and phenolics, and worsening water quality. Eukaryotes exhibited higher α-diversity and more complex co-occurrence networks, showing greater responsiveness to disturbance. Stochastic processes dominated community assembly (>68%) for both eukaryotic and prokaryotic communities. Dispersal limitation led to higher total β-diversity and nestedness in eukaryotes; by contrast, land use intensified environmental filtering on prokaryotes, resulting in lower β-diversity but higher turnover contribution. Community disassembly simulation reveals a scenario in which impervious surface expansion is associated with non-random species loss, reducing predicted functional richness of both eukaryotic and prokaryotic microbes; the preferential loss of sensitive species is associated with a sharp decline in predicted functional richness, which may have implications for ecosystem stability. Our findings demonstrate that land use change is significantly associated with altered aquatic environments and affects ecosystem functions through biodiversity changes, providing theoretical support for ecosystem conservation.

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.

As the largest tributary of the Yangtze River and a core area of the Middle Route of the South-to-North Water Diversion Project, the Han River Basin holds significant ecological importance regarding the impacts of land use and water environment changes on aquatic ecosystems. Existing studies have mostly focused on local reaches of the upper or middle–lower Han River, and systematic investigations into the associations between macroinvertebrate communities and environmental factors at the entire basin scale remain scarce. The niche characteristics and environmental drivers of macroinvertebrate community structure in the Han River Basin, China, were evaluated using a variety of diversity metrics and statistical methods. The results showed that: (1) A total of 91 macroinvertebrate taxa were identified during 2022–2023, with Insecta as the dominant group. Species richness in the upstream reaches increased in 2023, and the degree of differentiation between the upstream and the middle–lower reaches was markedly weaker than that in 2022. (2) Significant interannual differences in macroinvertebrate community structure were detected (PERMANOVA, p < 0.05), and taxa such as Polypedilum sp., Orthocladius sp., and Gammaridae collectively accounted for 35.6% of the dissimilarity among communities. (3) The overall niche breadth of dominant taxa was relatively low, whereas niche overlap decreased significantly in 2023, indicating a community niche pattern characterized by “low competition–high differentiation”. (4) Total phosphorus (TP) and total nitrogen (TN) were the core water environmental factors driving changes in community structure, while forested land was the key land use factor, and their synergistic effects jointly regulated the composition and diversity of macroinvertebrate communities.