Aside from the classical residues of persistent organic pollutants (POPs), the occurrence of emerging contaminants (ECs) in the environment has become a subject of increasing concern due to their harmful impact on the aquatic environment. Wastewater treatment plant (WWTP) effluents are major sources of environmental pollution. Therefore, data concerning their existence is required. In this study, twenty compounds representative of different drug groups considered ECs and belonging to antibiotics, antipsychotics, anti-inflammatory drugs plus acesulfame K were selected to be accurately detected and quantified with UHPLC–LTQ-Orbitrap MS in hospital and urban WWTP effluents. Chromatographic parameters (column efficiency, mobile phase, etc.), as well as mass spectrometry conditions concerning ionization mode and Orbitrap analysis (ESI options, mass resolving power, AGC target, tube lens, injection time), were evaluated. Moreover, a novel fabric phase sorptive extraction (FPSE) method based on fiber glass coated with PEG300 was employed as sample preparation process. Experimental parameters affecting extraction and desorption steps such as sample pH, extraction time, ionic strength, elution time and solvent have been optimized. The optimized methodology was validated providing excellent linearity (R2 > 0.99), and low detection and quantification limits up to 3.1 and 9.3 ng/L, for carbamazepine, respectively. Relative recoveries ranged from 81.1% to 114.0%, while a medium matrix effect for most of the target compounds occurred. Applying the above analytical method in effluents of WWTPs from NW Greece, nine compounds were quantified with concentrations that varied from 55.4 to 728.4 ng/L.