Through a series of long-term column experiments, the fate of three common pharmaceuticals (carbamazepine (CBZ), diclofenac, and indomethacin) and their major phase I metabolites in soil aquifer treatment (SAT) were monitored. CBZ concentration increased by a factor of two (from 37 to ca. 70 ng/L) regardless of the treatment conditions, and its metabolites, 10,11-dihydro-10hydroxycarbamazepine (approximately 500 ng/L after SAT) and CBZ-10,11-epoxide (12-42 ng/L after SAT) were not effectively removed after SAT. Our results indicated that some metabolites of pharmaceuticals are present at much higher concentration than the original forms in the SAT effluent, and that some metabolites are more persistent during SAT with a relatively short retention time (i.e., 30 days). The study indicated that more attention should be paid to the formation and fate of metabolites in the water quality management of SAT effluent.