A sensitive and robust method of analysis for quaternary ammonium compounds (QACs) in marine sediments is presented. Methods for extraction, sample purification, and HPLC-time-of-flight MS analysis were optimized, providing solutions to problems associated with analysis of QACs, such as dialkyldimethylammonium (DADMAC) and benzalkonium (BAC) compounds experienced previously. Recognized in this study are the exceptionally high positive mass defects characteristic of alkylammonium or protonated alkylamine ions. No alternative and chemically viable elemental formulas exist within 25.2 mDa when the number of double bond equivalents is low, effectively allowing facile discrimination of this compound class in complex mixtures. Accurate mass measurements of diagnostic collision-induced dissociation fragment ions and heavy isotope peaks were obtained and also seen to be uniquely heavy compared to other elemental formulas. The ability to resolve masses of alkylamine fragment ions is much greater than for the molecular ions of BACs and many other chemicals, opening up a range of potential applications. The power of utilizing a combination of approaches is illustrated with the identification of nontargeted DADMAC C8:C8 and C8:C10, two widely used biocides previously unreported in environmental samples. Concentrations of QACs in sewage-impacted estuarine sediments (up to 74 microg/g) were higher than concentrations of other organic contaminants measured in the same or nearby samples, suggesting that further study is needed.