Climate change and eutrophication have significant impacts on aquatic ecosystems, with phytoplankton playing a critical role as primary producers. This study investigates the relationships between phytoplankton communities and environmental and meteorological factors in Wuliangsuhai Lake, a representative ecosystem in an arid and cold region of China. Using data from 25 sampling sites (April–September 2023), a generalized additive model (GAM) was employed to analyze water quality and laboratory measurements. The results showed a bimodal distribution of phytoplankton density, with peaks in July (5.33 × 106 cells/L) and August (14.90 × 106 cells/L). Green algae dominated in spring, while cyanobacteria became dominant in summer. GAM analysis revealed that temperature (TEMP) was the primary driver, explaining 20.7% of the deviance. When TEMP was examined together with other factors, the explanatory ability of the model was significantly enhanced, and finally, the model explained 57.10% of the deviance. GAM analysis also revealed that different algae species responded differently to environmental factors, with the cyanophyta-dominant species Pseudoalgae being more sensitive to TEMP and pH, whereas the chlorophyta-dominant species Chlorella was more affected by wind speed and salinity. Cyanobacteria dominance, exacerbated by warming, increases the risks of harmful algae blooms and ecosystem instability, highlighting the need for mitigation strategies in vulnerable freshwater ecosystems.