The reuse of discharged cooling tower water (CTW) in the cooling tower itself could reduce fresh water intake and help mitigating fresh water scarcity problems. However, this requires desalination prior to its reuse, and hindering fractions, such as conditioning chemicals, should be removed before desalination to obtain a higher desalination efficiency. Constructed wetlands (CWs) can provide such a pre-treatment. In this study, the mechanisms underlying the removal of conditioning chemical benzotriazole (BTA) in CWs was studied using an innovative approach of differently designed pilot–scale CWs combined with batch removal experiments with substrate from these CWs. By performing these combined experiments, it was possible to determine the optimal CW design for BTA removal and the most relevant BTA removal processes in CWs. Adsorption yielded the highest contribution, and the difference in removal between different CW types was linked to their capability to aerobically biodegrade BTA. This knowledge on the main removal mechanisms for BTA allows for a CW design tailored for BTA removal. In addition, the outcomes of this research show that performing batch experiments with CW substrate allows one to determine the relevant removal mechanisms for a given compound which results in a better understanding of CW removal processes.