The continuous release of metabolic pharmaceuticals and artificial sweeteners into aquatic environments has raised concerns due to their persistence and biological activity. Despite their widespread detection, the mechanistic effects of these contaminants on aquatic primary producers and their implications for ecosystem functioning remain insufficiently understood. This study assessed the ecotoxicological responses of three representative aquatic primary producers (Chlorella vulgaris, Nostoc sp., and Lemna minor) exposed to environmentally relevant concentrations of metformin (MET), its transformation product guanylurea (GUA), and the artificial sweeteners sucralose (SUC) and acesulfame-K (ACE-K). Acute (72 h) and subchronic (7 d) exposures were conducted to evaluate growth, photophysiology (Fv/Fm, ETR, NPQ), oxidative stress biomarkers, nitrogen metabolism, and detoxification-related responses. Mixture experiments were performed under subchronic conditions to assess the interaction effects. MET and GUA produced the strongest physiological disturbances across species, including reduced electron transport and nitrogen assimilation, and increased oxidative stress. Artificial sweeteners induced comparatively weaker but significant responses in the participants. Subchronic exposure amplifies physiological disruption relative to acute conditions. Multivariate analysis revealed coordinated responses linking photophysiology, the redox balance, and nitrogen metabolism. Mixture exposure resulted in predominantly additive to moderately synergistic effects, particularly on oxidative stress and photochemical efficiency, with MET and GUA acting as dominant drivers. Metabolic contaminants disrupt interconnected physiological pathways in aquatic primary producers, potentially affecting primary productivity and nutrient cycling. These findings highlight the importance of integrating sublethal and multi-species responses into ecotoxicological risk frameworks, particularly under realistic mixture exposure scenarios.