Gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (LC-APCI-MS) were optimized and applied for the trace-level determination of 42 priority pesticides and 33 priority organic pollutants from European Union Directive EC 76/464. First, off-line solid-phase extraction of 200 ml of river water using an OASIS solid-phase extraction cartridge, followed by GC-MS was used. Next, selected samples that were positive to GC-MS were analyzed by LC-APCI-MS in order to detect further polar byproducts or to improve the determination of previously detected polar analytes. The transformation products of triazine pesticides like deethylatrazine (DEA) and deisopropylatrazine (DIA) and compounds such as diuron and several chlorophenols were positively identified by LC-APCI-MS. The present methodology has also been used for searching for new analytes not included in the EC 76/464 list, like Irgarol, DEA and DIA. In addition it was applied to target pollutants in 43 river water samples from Portugal during a pilot survey from April to July 1999. Atrazine followed by simazine and 2,4,6-trichlorophenol were the most ubiquitous compounds detected in this area. The levels detected of the different compounds were in the range of: 0.01-2.73 microg/l, 0.05-0.74 microg/l, 0.02-1.65 microg/l, 0.02-5.43 microg/l, 0.01-0.40 microg/l, 0.01-0.26 microg/l, 0.02-0.61 microg/l, 0.01-3.90 microg/l, 0.01-1.24 microg/l, 0.02-2.3 microg/l, 0.01-0.13 microg/l and 0.01-0.5 microg/l for atrazine, simazine, terbuthylazine, alachlor, metolachlor, Irgarol, propanil; tributhylphosphate, diuron, 2,4,6-trichlorophenol, deisopropylatrazine and deethylatrazine, respectively.