The growth and reproduction of phytoplankton are closely associated with the changes of water environment; thus, phytoplankton have been taken as environmental indicator organisms and provided references for water environment protection. However, the phytoplankton community characteristics of Dianchi Lake (a seriously polluted lake in China) are unclear under the background of the cumulative effects of historical pollutants and current control measures, and environmental DNA (eDNA) metabarcoding monitoring has rarely been applied in phytoplankton research at Dianchi Lake. Therefore, this study investigated the temporal and spatial characteristics of phytoplankton community and the environmental stressors of Dianchi Lake via eDNA metabarcoding monitoring. A total of 10 phyla, 22 classes, 50 orders, 82 families, 108 genera and 108 species of phytoplankton were detected, and distinct temporal and spatial variations in the phytoplankton community (e.g., ASV number, dominant taxon, the relative abundance) were observed in Dianchi Lake. Microcystis dominated the prokaryotic phytoplankton community from the dry period to the wet period, but interestingly, the first dominant cyanobacteria genus was changed from Microcystis (dry period) to Planktothrix (wet period). Cryptophyta dominated in the eukaryotic phytoplankton community from the dry period to the wet period, and eukaryotic-phytoplankton-dominant genera included Cryptomonas, Aulacoseira, Plagioselmis and others. A temporal–spatial heterogeneity of the relationships between the phytoplankton community and environmental factors was shown in Dianchi Lake. Dissolved oxygen was the crucial environmental stressor influencing the phytoplankton community structure in Dianchi Lake during the dry period, while pH was the crucial one during the wet period. The impacts of total phosphorus and nitrogen also showed differences at different periods. This research provides an interesting perspective on phytoplankton diversity monitoring and the health assessment and restoration of Dianchi Lake.

As environmental indicators, invertebrate communities are closely related to changes in the water environment. Efficient and accurate monitoring of invertebrates is of great significance for providing references for water environment conservation. However, environmental DNA metabarcoding has rarely been used in invertebrate research at the Chai River in Kunming, Yunnan, China, and the current characteristics of invertebrate communities are unclear. Therefore, this study investigated the spatial and seasonal patterns of invertebrates and the environmental stressors of the Chai River. Based on eDNA metabarcoding, 873 ASVs of invertebrates belonging to Annelida, Arthropoda, Cnidaria, Gastrotricha, Mollusca, Nematoda, Platyhelminthes, Protozoa, and Rotifera were identified, with Arthropoda being the absolute dominant phylum. Distinct spatial and seasonal variations in the invertebrate communities (e.g., ASV number, dominant genera, relative abundances) were observed. Macrothrix and Acanthamoeba were the first and second most dominant genera, both in dry and wet periods. A spatial–seasonal heterogeneity of the relation between the invertebrate communities and environmental factors was observed in the Chai River. The water temperature (WT), chemical oxygen demand (COD), conductivity (C), and Chlorophyll-a (Chl-a) levels were deemed to be the crucial environmental factors influencing the distributions of invertebrate communities in the Chai River, which was consistent with the spatial and seasonal differences in pollution characteristics around the Chai River. This study provides insights into conserving the diversity of invertebrate communities and the management of the Chai River and similar agricultural rivers.