Thiol compounds (R–SH) have many important biological functions and are principal controls of the speciation of several toxic metals in the environment. However, determining the concentration of thiols associated with environmental matrices is challenging due to the compounds’ low abundance and interferences from non-thiol compounds for many available methods. Here a novel method has been developed and validated to quantify the total concentration of thiol functional groups in aqueous samples using derivatization with monobromo(trimethylammonio)bimane (qBBr) and quantification with tandem mass spectrometry. The thiol concentration was determined by titration of the sample with qBBr, which reacts selectively with thiols, and quantification of the residual qBBr. We systematically evaluated potential interferences from various organic compounds, inorganic ions (including sea water matrices), sulfide and mercury (Hg) species, and demonstrate that the method is highly sensitive, selective and robust. The limit of detection (LOD) for total thiols is in the nanomolar concentration range (~6 nM). The method performance was also demonstrated by determination of the total thiol concentration in different natural samples including boreal stream water (1.16 μM), wetland porewater (0.96 μM) and the Suwanee River natural organic matter (NOM) reference material SR101 N (7.9 μmol g−1). The developed method represents a combination of low LOD and high selectivity and robustness that is unsurpassed for total thiol concentration measurements.