The primary drawback of reusing treated wastewater for irrigation is that most wastewater treatment plants (WWTPs) remain unable to remove most emerging pollutants detected in recent decades, necessitating a strategy to improve these WWTPs’ performance. In this regard, the present study aims to evaluate the effectiveness of an enhanced pilot vertical-flow biochar-enriched constructed wetland for treating municipal wastewater pretreated with natural lagoons. Three key harmful micropollutants are addressed: heavy metals (trace elements), pharmaceutical residues, and antibiotic-resistant bacteria (ARB). The system utilizes a biochar layer to enhance treatment efficiency by increasing adsorption capacity and supporting beneficial microorganisms, in conjunction with Phragmites australis plants that facilitate oxygen transfer and nutrient uptake. To evaluate the treatment system’s performance, Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was used to measure heavy metal concentrations. A molecular approach using quantitative polymerase chain reaction (qPCR) was used to quantify antibiotic resistance genes (ARGs) in water samples before and after treatment, including β-lactamases TEM, CTX-M, and SHV. The performance obtained is remarkable for the well-known toxic metals, reducing their concentrations from 16.35 ± 0.82 μg L ^-1 for arsenic, 0.0936 ± 0.0047 μg L ^-1 for cadmium, and 0.6036 ± 0.030 μg L ^-1 for lead to 2.75 ± 0.14 μg L ^-1 , 0.0014 ± 0.000070 μg L ^-1 , and 0.089 ± 0.0045 μg L ^-1 , respectively. Furthermore, the results showed a significantly reduced copy number of the 16S rRNA gene and of the resistance-conferring genes. Pharmaceutical residues (doxycycline, ciprofloxacin, enoxacin, enrofloxacin, norfloxacin, ofloxacin, amoxicillin and ampicillin) were also effectively removed after treatment, with removal rates ranging from 63% to over 99% depending on the compound. For example, ibuprofen and ciprofloxacin were reduced by 96%–97% (from 7.310 to 238 ng L ^-1 and from 2.300 to 83 ng L ^-1 , respectively). Even recalcitrant molecules such as carbamazepine and diclofenac have been reduced by more than 60%, confirming the high efficiency of the biochar-enriched artificial wetland system. These results highlight the considerable potential of this nature-based solution as a promising approach to addressing the global concern of enhancing WWTP removal of emergent pollutants. It therefore offers a sustainable, environmentally friendly alternative for wastewater treatment reuse in irrigation.