A novel methodology was developed for the determination of alkyl (C-12, C-14, and C-16) dimethylbenzylammonium chloride (benzalkonium chloride Dr BAG, Chemical Abstract Service number: 8001-54-5) in water samples. This method is based on solid-phase extraction (SPE) using polymeric cartridges, followed by high-performance liquid chromatography/ion trap mass spectrometry (LC/MS) and tandem mass spectrometry (MS/MS) detection, equipped with an electrospray interface in positive ion mode. Chromatographic separation was achieved for three BAC homologues by using a Cis column and a gradient of acetonitrile/10 millimolar aqueous ammonium formate. Total method recoveries were higher than 71% in different water matrices. The main ions observed by LC/MS were at mass-to-charge ratios (m/z) of 304, 332, and 360, which correspond to the molecular ions of the C-12, C-14, and C-16 alkyl BAG, respectively. The unequivocal structural identification of these compounds in water samples was performed by LC/MS/MS after isolation and subsequent fragmentation of each molecular ion. The main fragmentation observed for the three different homologues corresponded to the loss of the toluyl group in the chemical structure, which leads to the fragment ions at m/z 212, 240, and 288 and a tropylium ion, characteristic of all homologues, at m/t 91. Detection limits for the methodology developed in this work were in the low nanogram-per-liter range. Concentration levels of BAG-ranging from 1.2 to 36.6 micrograms per liter-were found in surface-water samples collected downstream from different wastewater-treatment discharges, thus indicating its input and persistence through the wastewater-treatment process.