In this study, molecular weights of thiols from four laboratory cultures (Scenedesmus obliquus, Chlorella vulgaris, Euglena gracilis, and Attheya septentrionalis) and the Churchill River (Manitoba) were assessed using a fluorescent-labeling method such as monobromotrimethylammoniobimane (qBBr) and asymmetrical flow field-flow fractionation (AF4) coupled to a fluorescence detector. Concentrations of thiols in extracellular fractions ranged from 6.39 ± 3.39 to 39.2 ± 7.43 μmol g(-1), and intracellular concentrations ranged from 11.5 ± 4.52 to 41.0 ± 4.1 μmol g(-1). In addition, molecular weights (MW) of intracellular thiol ranged from 493 ± 24 to 946 ± 12 Da whereas extracellular thiol MWs varied from 443 ± 36 to 810 ± 174 Da. The novel method of combining AF4 to an on-line fluorometer and the incorporation of the thiol tag provided information regarding thiol concentration and composition of controlled and natural systems. Furthermore, the proposed methods allow for the simultaneous measurement of thiol and DOM MWs produced by microorganisms. By assessing characteristics of naturally produced thiols and lab-grown thiols, information regarding heavy metal complexation can be determined.