A comprehensive method has been developed and validated in two different water matrices for the analysis of 16 pharmaceutical compounds using solid phase extraction (SPE) of water samples, followed by liquid chromatography coupled with tandem mass spectrometry. These 16 compounds include antibiotics, hormones, analgesics, stimulants, antiepileptics, and X-ray contrast media. Method detection limits (MDLs) that were determined in both reagent water and municipal tap water ranged from 0.1 to 9.9 ng/L. Recoveries for most of the compounds were comparable to those obtained using U.S. EPA methods. Treated and untreated water samples were collected from 31 different water treatment facilities across Missouri, in both winter and summer seasons, and analyzed to assess the 16 pharmaceutical compounds. The results showed that the highest pharmaceutical concentrations in untreated water were caffeine, ibuprofen, and acetaminophen, at concentrations of 224, 77.2, and 70 ng/L, respectively. Concentrations of pharmaceuticals were generally higher during the winter months, as compared to those in the summer due, presumably, to smaller water quantities in the winter, even though pharmaceutical loadings into the receiving waters were similar for both seasons.