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The degradation and metabolic pathways of sulfamethazine (SMZ) and enrofloxacin (ENR) via microalgal treatment systems were investigated in this study. SMZ and ENR applied at 1–25 mg L−1 did not significantly inhibit the growth of Chlorella vulgaris or Scenedesmus obliquus. SMZ and ENR exposure did not significantly alter the maximum quantum efficiencies of C. vulgaris and S. obliquus. When cultured at light intensities of 45–50 μmol photon m−2 s−1, the C. vulgaris and S. obliquus treatment systems achieved 24% and 11% degradation, respectively. The greatest removal of ENR was 52% and 43.3%, for C. vulgaris and S. obliquus treatment systems, respectively, after 15 days. The results indicated that the degradation of SMZ and ENR occurred by a combination of biodegradation and photolysis. Kinetic investigations revealed that the removal of SMZ and ENR (5 mg L−1) followed a first-order model, with apparent rate constants (k) ranging from 0.0141 to 0.0048 day−1 and 0.0132 to 0.0086 day−1, respectively. Fifteen metabolites of SMZ and five intermediates of ENR were identified by UPLC-MS, and degradation pathways for SMZ and ENR were proposed. SMZ transformation reactions included ring cleavage, hydroxylation, methylation, and oxidation, whereas ENR was degraded by dealkylation, decarboxylation, and defluorination.