To evaluate the change trends of plankton in inland saline–alkaline water bodies, this study investigated the ecological restoration and rational development of saline–alkaline lakes in northwest China. From June to October 2023, phytoplankton communities in a high-salinity lake in Alar City, Xinjiang, were analyzed using standard survey methods for inland natural waters. Biodiversity indices were calculated, and redundancy analysis (RDA), Spearman’s correlation analysis, and Mantel test were carried out to assess the functional community structure of phytoplankton and its environmental drivers. In total, 115 phytoplankton taxa belonging to seven phyla were identified. The densities ranged from 23.76 × 10⁵ to 53.54 × 10⁷ cells/L. Bacillariophyta and Cyanophyta were the dominant phyla, accounting for 41.7% and 27.8% of the total taxa, respectively. The dominant species included Microcystis spp., Merismopedia sp., Cyclotella meneghiniana, and other algae. Spearman correlation analysis revealed that salinity, water temperature (WT), Na⁺, TDS, HCO₃⁻, Cl⁻, and K⁺ were key environmental factors significantly influencing phytoplankton community structure. Mantel tests confirmed that salinity (SAL), TDS, DO, and major ions (K⁺, Na⁺, CO₃²⁻) served as key determinants of spatiotemporal phytoplankton community distribution (p < 0.05). RDA results indicated that WT, TDS, alkalinity (ALK), pH, salinity, and Na⁺ were the key factors driving seasonal variations in phytoplankton communities. Notably, decreasing salinity and ion concentrations stabilized the phytoplankton community structure, maintaining high-diversity indices. This highlights the positive impact of ecological restoration measures, such as fisheries-based alkalinity control and systematic environmental management, on the health of saline–alkaline lake ecosystems. These findings provide important insights for the sustainable development of saline–alkaline fisheries and the conservation of aquatic biodiversity in arid regions.

EDNA metabarcoding has been used for the biomonitoring of benthic invertebrates, but the correct steps to achieve its effectiveness, the stability of the results, and comparisons with morphological methods are still understudied. In this study, morphology and eDNA were studied for benthic invertebrate samples collected at six sites in the Ulungu River Basin. A Mantel test and NMDS analyses were used to test the correlations of the communities obtained via the two methods, the Shannon index was calculated to evaluate the ecological status, and the correlation of the evaluation results was analyzed. The results revealed that eDNA metabarcoding did not detect a greater number of species than the morphological method, that the results from the two methods shared fewer taxa at the family level and below, and that only five taxa were shared at the genus level. The Mantel test and NMDS analyses revealed very significant differences between the communities monitored by the two methods (PERMANOVA, p = 0.0056), but eDNA metabarcoding provided richness and abundance data for species that are difficult to identify morphologically, and these findings can be used to supplement the morphological data. The cor.test revealed that there was no significant correlation between the diversity and ecological assessment results of the two methods, and the ecological assessment results of eDNA metabarcoding cannot represent accurate and true ecological conditions. The water sample eDNA-based method and morphological method exhibited low consistency and high complementarity in monitoring benthic invertebrate communities and diversity. More research is still needed on the key links of eDNA sampling, the control of the degradation rate, data utilization, and index development to provide more environmentally friendly and effective monitoring methods for ecological protection, more reliable support for ecological decision-making, and to more adequately respond to the challenges of global environmental change.