This study elucidated the complex drivers influencing plankton community structure in Lake Bolmen, a critical freshwater resource for drinking water production. The study investigated the relative contributions of per- and polyfluoroalkyl substances (PFAS) and a suite of environmental parameters (pH, water temperature, dissolved oxygen, conductivity, turbidity, chlorophyll, total dissolved solids, salinity, total nitrogen, and total organic carbon) on the phytoplankton and zooplankton community composition in Lake Bolmen. By analyzing PFAS concentrations, a range of environmental parameters, and plankton community composition from nine sites, the study found that both environmental factors and PFAS significantly determine plankton community composition. While PFAS concentrations were strongly correlated with salinity, they did not show significant correlations with any other of the measured water quality parameters. Principal Component Analysis (PCA) and Canonical Correspondence Analysis (CCA) revealed specific relationships between environmental parameters and PFAS with various plankton genera, indicating their preferences for certain conditions. Specifically, the plankton genera Pinnularia, Tabularia, Pediastrum, Stauroneis, Aphanizomenon flosaquaqe, Scendesmus, Dinobyron, Gymnozya, Synedra capitata, Synura and Chydorus are showing strong association with the PFAS and environmental parameters. The study underscores the necessity of integrated environmental assessments, considering both traditional water quality parameters and emerging contaminants like PFAS, to effectively monitor and manage lake ecosystem health.