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Non-steroidal anti-inflammatory drugs are the group of pharmaceuticals that is most often found in the environment, whereas estrogenic hormones are considered to be potent endocrine disruptors. However, the fate and persistence of these compounds in the environment are still unclear. In this study we propose two approaches for determining these compounds in environmental water samples: GC–MS using time windows and operating in selected ion-monitoring mode (SIM) and, for the first time, gas chromatography with electron capture detection (GC–ECD). The identification criteria of both methods fulfilled the requirements of Directive 2002/657/EC. The use of time windows improved the sensitivity of GC–MS measurements. In GC–MS analysis the pharmaceuticals were determined as trimethylsilyl, in GC–ECD as pentafluoropropionyl derivatives. The influence of such parameters as the type of reagent, type of …