
Nanoplastics (NPs) are emerging contaminants in freshwater ecosystems, readily forming heterogeneous aggregates with microalgae, yet their behavior in algal phycospheres remains poorly resolved. Here, we establish an aquatic phycosphere−plastic symbiotic system and a four-tiered analytical workflow, encompassing growth responses, cellular effects, phycosphere dynamics, and proteomic reprogramming to test how surface charge controls interactions between carboxylated and aminated polystyrene NPs (PS-COOH, PS-NH2, 50 nm) and Chlorella pyrenoidosa. Negatively charged PS-COOH exposure largely preserved physiological, ultrastructural, and redox homeostasis, indicating high tolerance of the symbiotic system. In contrast, positively charged PS-NH2 strongly inhibited biomass and chlorophyll, and triggered a cascade of intracellular stress, including sustained reactive oxygen species (ROS) production, lipid peroxidation, antioxidant imbalance, mitochondrial membrane depolarization, and up to 89.6% apoptosis. Three-dimensional excitation−emission fluorescence with parallel factor analysis and self-organizing map (PARAFAC-SOM) analysis revealed charge- and dose-dependent reorganization of tyrosine- and tryptophan-like protein components in tightly and loosely bound extracellular polymeric substances, indicating spatial eco-corona remodeling. Quantitative proteomics showed that PS-COOH mainly induced homeostasis regulation in photosystem and electron-transport proteins, whereas PS-NH2 broadly disrupted photosynthesis, carbon metabolism, and protein homeostasis. This multitier framework links NPs’ surface charge to coupled interfacial, cellular, and proteomic processes in microalgal phycospheres, providing a mechanistic basis to assess the biological footprint of NPs in freshwater ecosystems.