An analytical procedure involving solid-phase extraction (SPE) and gas chromatography–mass spectrometry (GC–MS) has been developed for determination of pharmaceutical compounds (aspirin, caffeine, carbamazepine, diclofenac, ketoprofen, naproxen, ibuprofen, clofibrate, clofibric acid, and gemfibrozil) in a variety of aqueous samples (wastewater and surface water). After filtration, samples were extracted and concentrated using C18 or HLB cartridges, depending on the type of compound. Sample storage conditions were checked and optimized to ensure preservation of the pharmaceutical substance, taking into consideration environmental sampling conditions. For most of the pharmaceuticals monitored, recovery was in the range 53 to 99% and the variability was below 15% for the complete procedure, with limits of detection ranging from 0.4 to 2.5 ng L−1, depending on the compound. The methods were successfully applied to monitoring of pharmaceutical contamination of the Seine estuary. Concentrations varied from several dozens of nanograms per liter for surface waters to several hundreds of nanograms per liter for wastewaters.