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The occurrence of human and veterinary pharmaceutical compounds in surface waters (e.g. streams, lakes and reservoirs) is an important emerging environmental issue. There is a need for robust, sensitive and reliable analytical methods for measuring these compounds in a variety of natural water and wastewater matrices. This paper describes a method for the determination of seven tetracycline (TC) and six sulfonamide (SA) compounds in pristine and wastewater-influenced surface water using solid-phase extraction, and LCQ Duo ion trap liquid chromatography/tandem mass spectrometry (LC/MS/MS) with positive electrospray ionization (ESI(+)) and selected reaction monitoring (SRM). The seven TCs and six SAs analyzed using this method include oxytetracycline (OTC), chlortetracycline (CTC), tetracycline (TC), democlocycline (DMC), doxycycline (DXC), meclocycline (MCC), minocycline (MNC), sulfathiazole (STZ), sulfamerazine (SMR), sulfamethazine (SMT), sulfachloropyridazine (SCP), sulfamethoxazole (SMX), and sulfadimethoxane (SDM). This study discusses the effects of flow rate, LC column diameter and LC column temperature on UV and/or mass peak quality of the different analytes. Several product ions for MS/MS detection have been identified and compared for ion trap and triple quadrupole LC/MS/MS instruments. Statistical analysis for determination of the method detection limit (MDL), accuracy and precision of the method is described. Matrix effects are evaluated in deionized, pristine and wastewater-influenced river water. The method is applied to evaluate the occurrence of these compounds in a small watershed in northern Colorado.