Among the release solutions for reducing the discharge of organic and persistent contaminants in the aquatic environment, the use of a tertiary treatment in addition to existing conventional wastewater treatment processes is considered. The use of micro-grain activated carbon in a fluidized bed is a promising technique investigated in this study. The effluents from a large-scale pilot system were analyzed by liquid chromatography coupled with high-resolution mass spectrometry (QToF). Several strategies were deployed, namely molecular fingerprint comparison, suspected and non-target analyses, identification of refractory compounds to treatment, and finally, quantification of identified compounds. The evaluation of the molecular fingerprints provided evidence of the overall effect of the tertiary treatment on the treated wastewater quality. The suspected approach highlighted the presence of 83 pharmaceuticals and pesticides as well as transformation products in the effluents. The non-target approaches also highlighted compounds refractory to tertiary treatment, such as illicit drugs or some pharmaceuticals. The identification and quantification of identified compounds underscored the suitability of micro-grain activated carbon in eliminating many classes of pharmaceuticals with various physicochemical properties, such as anti-hypertensive, analgesic, anti-viral, antidepressant and even various pesticides.