The scarcity of data about the occurrence of pharmaceuticals in water bodies in Malaysia prompted us to develop a suitable analytical method to address this issue. We therefore developed a method based on solid-phase extraction combined with liquid chromatography-time of flight/mass spectrometry (SPE-LC-TOF/MS) for the analysis of sixteen prescribed and two nonprescribed pharmaceuticals that are potentially present in water samples. The levels of these pharmaceuticals, which were among the top 50 pharmaceuticals consumed in Malaysia during the period 2011-2014, in influent and effluent of five sewage treatment plants (STPs) in Bangi, Malaysia, were then analyzed using the developed method. All of the pharmaceuticals were separated chromatographically using a 5 μm, 2.1 mm × 250 mm C18 column at a flow rate of 0.3 mL/min. Limits of quantification (LOQs) were 0.3-8.2 ng/L, 6.5-89 ng/L, and 11.1-93.8 ng/L in deionized water (DIW), STP effluent, and STP influent, respectively, for most of the pharmaceuticals. Recoveries were 51-108%, 52-118%, and 80-107% from the STP influent, STP effluent, and DIW, respectively, for most of the pharmaceuticals. The matrix effect was also evaluated. The signals from carbamazepine, diclofenac sodium, and mefenamic acid were found to be completely suppressed in the STP influent. The signals from other compounds were found to be influenced by matrix effects more strongly in STP influent (enhancement or suppression of signal ≤180%) than in effluent (≤94%). The signal from prednisolone was greatly enhanced in the STP influent, indicating a matrix effect of -134%. Twelve pharmaceuticals were frequently detected in all five STPs, and caffeine, prazosin, and theophylline presented the highest concentrations among all the pharmaceuticals monitored: up to 7611, 550, and 319 ng/L in the STP influent, respectively. To the best of our knowledge, this is the first time that prazosin has been detected in a water matrix in Malaysia. Graphical abstract ᅟ.