The main objective of this study was to apply multivariate analysis, such as principal component analysis (PCA), to determine the influence of water quality parameters on the removal of triclosan (TCS) and ibuprofen (IB) in vertical subsurface flow constructed wetlands (VSSFs). For this purpose, two VSSFs were operated under TCS and IB concentrations of 10 μg/L. One VSSF system was planted with Agapanthus africanus and the other was left unplanted and used as a control. To determine the influence of water quality parameters on TCS and IB removal, the removal efficiencies for TCS, IB, organic matter and nutrients in VSSF systems were determined. Using these data, PCA was performed. The TCS and IB removal efficiencies in VSSF systems were found to vary between 60%–85% and 50%–84%, respectively. Regarding the effects of water quality parameters on TCS and IB removal, PCA showed that TCS removal has a strong association with the oxidation–reduction​ potential. This result confirms that aerobic conditions for VSSF systems promote the removal of the TCS compound. For the case of IB, an association between IB and biological oxygen demand removal was observed. However, this relation was found to be not significant. This study reveals that PCA allows us to determine the association between different variables in VSSF systems. Moreover, this work will serve as the basis for future research for optimizing the performance for removing TCS and IB by focusing on the improvement of aerobic conditions.