A new method based on ultra-performance liquid chromatography (UPLC) quadrupole time-of-flight mass spectrometry ((Q-ToF)-MS) was developed for the analysis of 32 biologically active compounds including anti-inflammatories, analgesics, lipid regulators, psychiatric drugs, anti-ulcer agents, antibiotics, beta-blockers and phytoestrogens. This new method allows chromatographic analysis in 14 min, with instrumental detection limits from 2 to 84 pg, and limits of quantification ranging from 0.1 to 15 ng/L in tap water, and from 2 to 300 ng/L in wastewater. The potential of liquid chromatography with triple quadrupole mass spectrometry (LC/QqQ-MS) was compared with that of UPLC/(Q-ToF)-MS for the analysis of biologically active compounds in water samples. LC/Q-ToF provides accurate mass information and a significantly higher mass resolution than quadrupole analyzers. The available mass resolution of ToF instruments diminishes the problem of isobaric interferences and helps the analysis of trace compounds in complex samples. In this work UPLC/Q-ToF chromatograms were recorded containing full scan spectral data. The m/z values of analytes were extracted from the total ion chromatogram (TIC) and the accurate masses of the compounds were obtained. In addition, to increase the selectivity of ToF measurements a narrow accurate mass interval (20 m m/z units mass window) was used to reconstruct the chromatographic traces. However, regarding quantitative performance in terms of dynamic range and limits of detection (LODs), typical LODs achieved by QqQ instruments operating in multiple-reaction monitoring (MRM) mode ranged from 1 to 50 ng/L in wastewater, and the linear response for QqQ instruments generally covers three orders of magnitude. This is an important advantage over ToF instruments and one of the reasons why QqQ instruments are widely used in quantitative environmental analysis.