As a suitable way for routine screening of pesticides and control of other organic contaminants in water, the combination of liquid chromatography triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS) and liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) has been applied to the analysis of 63 surface and waste water samples after conventional solid-phase extraction (SPE). The extracts were screened for 43 pesticides or degradation products by LC-QqQ-MS/MS achieving limits of detection (LOD) ranged from 0.04 to 2ngL(-1). Of the 43 selected pesticides, 33 were detected in water samples. The ESI-QTOF MS instrument was run using two simultaneous acquisition functions with low and high collision energy (MS(E) approach) and acquiring the full mass spectra. A home-made database containing more than 1100 organic pollutants was used for substance identification. Around 250 of these compounds were available at the laboratory as reference standards. Five pesticides and 3 of their degradation products, different to those selected in the QqQ method, were detected by QqTOF-MS. Thirteen pharmaceuticals and two drugs of abuse were also identified in the samples. In practice, the sample preparation proved to be suitable for both techniques and for a wide variety of substances with different polarity. Mutual confirmation and evidence of co-occurrence of several other organic contaminants were the main advantages of the combination of both techniques.