River–lake confluence zones are shaped by inflow hydrology, evaporative concentration, and water mixing, providing natural systems for examining phytoplankton responses to environmental gradients. Here, we investigated Siling Co and adjacent river–lake confluence zones at elevations above 4,500 m. We integrated genus-level phytoplankton cell-density and biomass data with 22 environmental variables from 14 sampling events at 10 sites, including seven Lake and seven River samples. Community diversity, composition, and community–environment associations were evaluated using ordination, permutation tests, correlation analyses, distance-based redundancy analysis, Mantel tests, and multi-method evidence integration. In total, 54 genera were recorded, with Bacillariophyta representing the dominant phylum. Lake and River samples overlapped in community composition, whereas sampling period explained more genus-level variation than water-body type. Major-ion and mineralization gradients were consistently associated with community turnover. pH and SiO₂ were associated with cell-density composition, whereas Cl⁻ was associated with biomass composition. Cyanobacterial relative biomass was positively correlated with total nitrogen and negatively correlated with SO₄²⁻. These findings indicate that phytoplankton community structure in the Siling Co river–lake confluence zone cannot be attributed simply to two discrete habitat types, namely lakes and rivers, and provide a new perspective on community assembly in extremely high-altitude river–lake confluence zones.

Phytoplankton are sensitive indicators of environmental change in high-altitude aquatic ecosystems, but their community responses across river–lake confluence zones remain insufficiently understood. We investigated phytoplankton community characteristics and environmental associations in the Siling Co river–lake continuum. This endorheic system lies above 4500 m, where river inflows, lake-water mixing, and evaporative concentration generate marked hydrochemical gradients. Genus-level cell density and estimated biomass were assessed with 22 environmental variables from 14 sampling events at 10 lake and river sites. We recorded 54 phytoplankton genera, with Bacillariophyta dominant. Lake and River samples overlapped in composition, whereas sampling period accounted for more community variation than water-body type. Major-ion and salinity-related gradients were associated with cell-density community dissimilarity after accounting for water-body type. Cell-density and biomass composition also showed partly distinct associations with pH and SiO₂, and with Cl⁻, respectively. These observations indicate that phytoplankton communities in the Siling Co river–lake confluence zone are more closely associated with sampling-period variation and hydrochemical gradients than with Lake/River habitat classification. These findings provide an initial basis for integrated biological and hydrochemical monitoring.