Two aerated horizontal subsurface flow treatment wetlands were studied over two years for the removal efficacy with respect of conventional wastewater parameters, micropollutants and effect-based methods. One wetland served as control and was aerated 24 h d⁻¹ across 100% of the fractional length of the system. The second aerated horizontal flow treatment wetland was investigated under several aeration modes: first year with a zone of 85% aeration, followed by five months with a zone of 50% aeration and six months with a zone of 35% aeration. With 85% aeration, no significant difference in the removal efficacy as compared to the fully aerated control could be observed, except for E. coli, which were removed four times better in the control. No significant difference in removal efficacy for Total Organic Carbon, 5-day Carbonaceous Biochemical Oxygen Demand, caffeine, and naproxen were observed. A 50% non-aerated zone reduced the overall removal efficacy of biological effects. The highest removal efficacy for the moderately biodegradable micropollutants benzotriazole and diclofenac was observed in the system with 50% aeration. This could be due to the sharp increase of dissolved oxygen (DO) and oxidation reduction potential at the passage from the non-aerated to the aerated zone (at 75% of the fractional length). The internal concentration profiles of caffeine, ibuprofen and naproxen varied from 12.5%, 25%, 50% to 75% fractional length due to redox shift, DO variations and other conditions. A reduction of the aerated zone to 35% of the fractional length results in reduced treatment efficacy for benzotriazole, diclofenac, acesulfame and biological effects but 50% aeration yielded as much degradation as the fully aerated control. These results indicate that less aeration could provide similar effluent water quality, depending on the pollutants of interest. E. coli and biological effects were removed best in the fully aerated system.