Determination of psychoactive substances (PAS) and/or their metabolites in surface waters is crucial for environmental risk assessment, and disclosure of their enantiomeric fractions (EF) allows discrimination between consumption, direct disposal, and synthesis pathways. The aim of this study was to develop and validate an indirect method by gas chromatography coupled to mass spectrometry (GC–MS) based on derivatization using (R)-(−)-α-methoxy-α-(trifluoromethyl) phenylacetyl chloride as chiral derivatization reagent, for enantiomeric quantification of amphetamine (AMP), methamphetamine (MAMP), 3,4-methylenedioxymethamphetamine (MDMA), norketamine, buphedrone (BPD), butylone, 3,4-dimethylmethcathinone (3,4-DMMC), 3-methylmethcathinone, and quantification of 1-benzylpiperazine and 1-(4-metoxyphenyl)-piperazine. The method allowed to evaluate the occurrence, spatial distribution, and the EF of the target chiral PAS in Portuguese surface waters and in effluents from 2 wastewater treatment plants (WWTP). For that, water samples were pre-concentrated by solid phase extraction using OASIS® MCX cartridges, derivatized and further analyzed by GC–MS. Both enantiomers of AMP, (R)-MDMA, (S)-MAMP, and the first eluted enantiomer of BPD (configuration not assigned) were found in surface waters, while effluent samples showed both enantiomers of MDMA, (S)-MAMP, (R)-AMP, and the first eluted enantiomer of BPD and 3,4-DMMC. According to our knowledge, this is the first multiresidue analytical method by CG–MS enrolling cathinones, amphetamines, and piperazines. The presence of illicit synthetic cathinones in Douro River estuary is here reported for the first time, along with other amphetamine derivatives. The potential of the method to monitor consumption of the target PAS was demonstrated.