This study investigated the removal of two model pharmaceutically active compounds (PhAcs), viz., ibuprofen and triclosan, in lab-scale engineered floodplain filtration (EFF) system. Biodegradation experiments were performed to acquire knowledge about the degradation of the targeted PhAcs, at an initial concentration of 350μg/L. Biodegradation results showed that the two compounds were bio-transformed to >70% after 15 days of incubation. Column tests were performed in a statistically significant manner to determine the adsorptive potential of the suggested filler layer in the EFF (C/C0), by varying the flow rate and initial concentration of the compound. It was observed based on the F and p-values that the main effects (F=3163, p<0.005) were more significant than the interactive effects (F=9561, p<0.05) for both ibuprofen and triclosan removal. Besides, by performing the Student's "t" test, it was concluded that the flow rate plays a major role in determining the rapidness of achieving complete breakthrough than the initial concentration of both the compounds. The data obtained from column studies under biotic conditions indicated that the removal mechanism for PhAcs is mainly biotransformation based, and that an EFF system may be effectively used to remove these emerging compounds during ground water recharge for water recycling. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.