The scientific significance of this work involved in investigating the removal of contaminants of emerging concern (CECs) and antibiotic resistance genes (ARGs) at pilot-scale with partially saturated vertical flow constructed wetland either bioaugmented or not with the Trichoderma asperellum (strain T34) by means of the non-target liquid chromatography high-resolution mass spectrometry and SmartChip™ Real-Time PCR methodological approaches. Bioaugmentation testing was successful as Trichoderma was able to grow in competitive conditions resulting from the use of secondary treated domestic wastewater. There was a clear relationship between the removal efficiency (RE) and the biodegradability as well as the sorption capacity of the identified compounds. The most easily eliminated compounds were those which are known to be readily biodegradable (e.g., nicotine). Interestingly, from 22 compounds with RE > 65%, 17 compounds have a log Dow between 0 and 3 (optimal plant uptake). The most significant beneficial effect was observed with benzotriazole and diclofenac. The most difficult compounds to be eliminated were the most polar ones (log Dow < 0) such as melamine. High variability in removal efficiency over the course of a four-week experiment remained the chief constraint for the proper assessment of treatment performances. Transformation products (TPs) were also investigated. N-oxide TPs and 14-hydroxyclarithromycin were formed in wetland treatment while TPs which were prone to undergo further N-dealkylation or hydroxylation reactions were partly eliminated. Bioaugmented wetland treatments caused a shift in the composition of ARGs but there was no statistical difference in average rates of ARGs removal.