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An analytical method based on solid-phase extraction followed by gas chromatography mass spectrometry (GC-MS) was developed and validated for the quantification of 39 pesticides with distinct physico-chemical characteristics (including some degradates), in estuarine water samples. The method includes pre-concentration of samples (2500-fold factor), in OASIS HLB cartridges, by solid phase extraction. The analysed pesticides included organochlorines, organophosphorous, triazines, pyrethroids and other miscellaneous compounds, that are usually analysed separately. Method detection limits were between 3.6 and 61.2 ng L-1. The obtained sensitivity and accuracy, associated with the inherent confirmatory potential of GC-MS, validate the method as a toll in environmental monitoring. Analyses of water samples (n = 84) taken from the Douro River estuary, from March to May 2009, showed the presence of all assayed pesticides, among which 71.6% where above the limits of quantification. Besides, the feasibility of the method for chemical monitoring was highlighted by establishing a first pattern of spatial-temporal fluctuation for all classes of pesticides in the estuary, showing a significant increase of their concentrations in April and mainly at the margin bordering the city of Porto. Moreover, the finding of environmental hazardous amounts of hexachlorbenzene, endrin, endosulfan (all forms), DDTs, chlorfenvinfos Z and simazine pose a clear risk for local aquatic wildlife, and eventually to humans, by direct exposure or by consumption of contaminated fish.