Abstract A robust and sensitive method for the detection of fluoroquinolones, sulfonamides and trimethoprim has been developed. Wastewater samples were acidified and extracted through an anion-exchange cartridge in tandem with a hydrophilic–lipophilic balance (HLB) cartridge, a procedure that reduced interferences from wastewater organic matter. The extracted antibiotics were analyzed using liquid chromatography electrospray mass spectrometry and selected ion monitoring. Quantification of antibiotics was assessed both by internal standard and standard addition methods. Average recoveries for a range of wastewater matrices were 37 to 129% for a 1 μg/L spiking concentration. The method detection limits (MDLs) of antibiotics in deionized water, final and secondary effluent ranged from 2 to 7 ng/L, from 20 to 50 ng/L, and from 30 to 90 ng/L, respectively. Assessment of matrix interference shows that signal suppression and MDL increases with higher amounts of organic matter in the sample. Analyses of samples from two municipal wastewater treatment plants indicate that ciprofloxacin, ofloxacin, sulfamethoxazole and trimethoprim are present in the secondary effluents at median concentrations of 100–160, 205–305, 395–575, and 40–705 ng/L, respectively.