Myclobutanil is a systemic fungicide belonging to the triazole group, which is frequently detected in environmental samples. Triticonazole, also a triazole fungicide, controls soil and seed-borne diseases and it is mainly used as a seed-coating pesticide. Both myclobutanil and triticonazole are considered as persistent pollutants in the environment, raising concerns about their environmental fate and ecotoxicity potential. The purpose of the present study was to investigate the efficiency of four pilot-scale horizontal subsurface flow (HSF) constructed wetlands (CWs) to remediate myclobutanil and triticonazole from artificially polluted water. Daily loading of the four CWs took place from March 2022 to July 2022 with contaminated water fortified with myclobutanil and triticonazole. Three of the CWs, encoded WMG-R, WMG-C, and WMG-U, with medium gravel (MG) as porous media and the fourth, with code name WFG-R, fine gravel (FG). Common reed (R, Phragmites australis) was planted in the WMG-R and WFG-R units, and cattail (C, Typha latifolia) in the WMG-C unit. The WMG-U unit with no plant was used as a control unit. The results showed that the removal rate follows the pattern: WFG-R (88.4%) > WMG-R > (83.4%) > WMG-C (59.3%) > WMG-U (36.6%) and WFG-R (88.5%) > WMG-C (71.0%) > WMG-R > (70.9%) > WMG-U (49.2%) for myclobutanil and triticonazole, respectively. The most significant factors influencing the fungicides’ dissipation were the porous media content and the plant species.