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A three-year study of the spatial and temporal variation of pesticide residues in Viotikos Kifissos basin (VKB), in central Greece, before and after the application of Low-Input Crop Management systems (LCM), was carried out between May 2009 and November 2011. A total of 253 water samples from 34 sampling points (boreholes, rivers, wells, vadose zone) were analysed for the presence of more than 200 pesticides and degradation products, using liquid and gas chromatography coupled to tandem mass spectrometry. Samples were prepared by solid-phase extraction (SPE) using Oasis HLB cartridges. Almost 70% of the samples were found positive for the presence of pesticides in amounts greater than the limit of detection. The most frequently detected pesticide was fluometuron, followed by s-metolachlor, metalaxyl-M, imidacloprid and ethalfluralin. The highest concentration was recorded for fluometuron (322g L-1), ethalfluralin (123g L-1) and s-Metolachlor (36.4g L-1). Results showed a reduction of the pesticides detected and quantified in water samples during 2011 compared to those measured in 2009 and 2010.