It is necessary to review changes in the interactions of indicators following the construction of the Three Gorges Dam (TGD) in order to explore the impact of the dam on ecology. Research on changes in interactions among indicators of the comprehensive social–economic–ecology system in the Yangtze River Basin is limited, and the objective of this study was to investigate how this system changed after the operation of the TGD, as well as how the indicators contributed to this change. Here, the correlational network approach using 38 data point indicators from 1949 to 2018 of the Yangtze River Basin was applied to analyze the changes in indicator interactions before and after the TGD operation. The TGD impoundment altered networks of the social–economic–ecological system in the Yangtze River Basin. Indicators are both less positively and less negatively connected. The number of synergy and trade-off networks clusters changed from two (Modularity = 0.33) to -six (Modularity = 0.23) and from two (Modularity = 0.015) to four (Modularity = 0.34) after the TGD operation, indicating that the sustainable development of the Yangtze River Basin might be at a middle level after the TGD operation. Further analysis revealed that the mean annual discharge, downstream fry runoff, and downstream counts of the eggs and larvae of four carp, diatom abundance index, breeding population of Chinese sturgeon, and annual precipitation contributed more to the changes in the networks after 2003.

Complete ammonia oxidizers (comammox) can completely oxidize ammonia to nitrate, and the various habitats of comammox Nitrospira are an important guarantee for their survival. The construction of the Three Gorges Dam, China, made it easier for nitrogen to stay in the reservoir area, which may have caused the niche differentiation of comammox, thereby affecting the natural transformation process of nitrogen in the reservoir area. This study investigated comammox in river sediments in the Three Gorges Reservoir area. Comammox clade A and comammox clade B were detected in all samples, and comammox clade A was dominant. The number of dominant OTUs (Operational Taxonomic Unit) in comammox clade A.1 accounted for 18.69% of the total number of OTUs, followed by comammox clade A.2 (18.58%) and clade B (14.30%). The indicated abundance of comammox Nitrospira clade A and clade B amoA genes in the main stream of the Three Gorges Reservoir increased along the length of the river and reached the maximum in the middle part of the reservoir area. The highest abundance of ammonia-oxidizing archaea (AOA) amoA genes appeared in the upper stream section of the reservoir area. Comammox Nitrospira clade A exhibited the highest abundance (3.00 × 10⁴ ± 8782.37 copies/g), followed by comammox Nitrospira clade B (1.83 × 10³ ± 1019.82 copies/g), ammonia-oxidizing bacteria (AOB) (1.28 × 10³ ± 574.69 copies/g), and AOA (1.73 × 10² ± 48.05 copies/g). The abundances of both comammox clades A and B were positively correlated with sediment pH, indicating that pH is an important environmental factor affecting the growth of comammox bacteria. Additionally, the relative abundances of both comammox clade A.2 and clade B were significantly correlated with overlying water dissolved oxygen (DO) in the reservoir area. This study thus indicated that there exists a niche differentiation of comammox Nitrospira in the main stream of the Three Gorges Reservoir area. The potential changes in the ammoxidation process and the environmental effects caused by this niche differentiation need further attention.

The construction of cascade hydropower stations on the lower Jinsha River has significantly altered natural hydrological regimes and ecological processes, posing potential impacts on aquatic ecosystems. Understanding the spatiotemporal dynamics of phytoplankton communities and their responses to environmental changes is crucial for the ecological management of reservoirs and the protection of water environments. This study investigated four cascade reservoirs in the lower Jinsha River during June (summer) and December (winter) 2023. Pronounced thermal and chemical stratification observed in June became homogenized in December, with concentrations of TN, NO₃-N, DTN, and TP significantly higher in December (p < 0.05) and accumulating downstream. Phytoplankton density generally decreased with increasing depth, and community structure differed significantly among the reservoirs (PERMANOVA, p < 0.05 except for WDD, p = 0.052). The density of Cyanophyta increased significantly from June to December (p < 0.05), whereas that of Bacillariophyta and Chlorophyta decreased. Mantel tests indicated significant correlations between phytoplankton communities and temperature, dissolved oxygen, and nitrate nitrogen (p < 0.05). Hierarchical partitioning revealed seasonal shifts in key driving factors: temperature (32.58%) and dissolved oxygen (20.13%) dominated in June, whereas nitrate nitrogen (21.86%) and suspended solids (15.22%) were the key factors in December. The elevated Cyanophyta density in December was associated with enhanced nutrient release from sediments, weakened dilution effects, and increased terrestrial inputs. This study reveals that phytoplankton community dynamics in subtropical cascade reservoirs are co-regulated by thermal stratification, nutrient availability, and seasonal changes. Future reservoir management strategies should prioritize monitoring thermal stratification and surface bloom risks in June, while focusing on controlling endogenous nutrient loading and optimizing water mixing processes in December. These findings provide important guidance for water quality management and ecological conservation strategies in regulated river systems. The online version contains supplementary material available at 10.1186/s12862-026-02502-2.