The present study advances our understanding of the ecological risk potential associated with pharmaceutical mixtures treated with fungal enzymes. We optimized a submerged bioreactor for fungal enzyme production by testing three fungal species and adjusting the organic loading rate and retention time, yielding enzyme activities exceeding 20 U/L. These fungal enzymes effectively reduced the half-lives of tetracycline and sulfamethoxazole to less than 3 h in a mixture of tetracycline and sulfamethoxazole, using syringaldehyde as an optimized mediator. Analytical chemistry assessments identified transformation products (TPs) generated in situ from the mixture, revealing three novel transformation pathways. Quantitative structure–activity relationship analysis highlighted two TPs with heightened toxicity and prolonged persistence compared to their parent compound. Furthermore, these TPs exhibited distinct environmental mobility characteristics at the liquid–solid interface. Our combined experimental and computational framework allowed for a systematic screening of pharmaceutical residues, considering aspects such as toxicity, mobility, persistence, bioaccumulation, and removal. This approach has practical implications for prioritizing target pollutants in subsequent monitoring and environmental risk assessments.