The occurrence of 28 pharmaceuticals and 10 estrogens has been investigated in waters from the lower part of the Llobregat River basin, where the main intakes for production of drinking water for Barcelona (Spain) are located. Sampling was programmed to monitor the same mass of water on its way down the river to reflect inputs from discharges, contribution from subsidiaries plus persistence of the compounds in the surface water. Analysis of pharmaceuticals was performed by off-line solid phase extraction (SPE) followed by liquid chromatography-tandem mass spectrometry with a triple quadrupole analyzer (LC-QqQ-MS/MS). Further analysis by ultra performance liquid chromatography-mass spectrometry with a time-of-flight analyzer (UPLC-TOF-MS) has been proposed and applied for confirmation of several of these target compounds. Estrogens have been analysed by on-line SPE-LC-QqQ-MS/MS. Within the class of pharmaceuticals, 23 out of the 28 compounds investigated, were detected in at least one sample. The highest concentrations were observed for the beta-blockers metoprolol (8042 ng L(-1)) and sotalol (788 ng L(-1)), the antibiotic ofloxacin (1904 ng L(-1)), and the lipid regulator gemfibrozil (1014 ng L(-1)). Within the group of estrogens, only estrone and estrone-3-sulfate were positively identified, with concentrations for the former (0.82-5.81 ng L(-1)) close in some locations to those considered sufficient to induce estrogenic effects in aquatic organisms (1-10 ng L(-1)). As a general pattern, concentration of target compounds increases along the river flow as expected. Copyright (c) 2010 Elsevier Ltd. All rights reserved.