Although reduced sulphur substances, such as thiol compounds, contain extremely reactive functional groups in the cell, and influence metal speciation and solubility, very few techniques have been developed to quantify such substances in natural waters. In this paper we present a novel method that allows for the simultaneous identification and quantification of glutathione (GSH), thioacetamide-like compounds (TA), and refractory organic matter (ROM) by differential pulse cathodic stripping voltammetry (DP-CSV). Organic compounds are initially deposited on a mercury drop electrode at 0.000 V, pH 1.95, in the presence of ~ 200 nmol L− 1 Mo(VI), and then stripped, creating reduction peak currents at specific potentials. Using a 60-s deposition time, limits of detection (LODs) are 1 nmol L− 1, 81 nmol L− 1 and 14 μg C L− 1 for GSH, TA and ROM, respectively. By increasing the deposition time to 300 s, LOD is decreased to 0.2 nmol L− 1, 22 nmol L− 1 and 2 μg C L− 1, respectively. This method has a number of advantages in terms of its rapidity, low cost, and relative simplicity (due to the lack of derivatization and pre-concentration steps) and is also an effective method for simultaneously analysing GSH, TA and ROM in water. When not mixed in solution, GSH, l-cysteine and N-acetyl-l-cysteine, as well as TA-like compounds and thiourea, can be detected and identified by measuring their peak potential and standard addition, due to the acidic pH, which also allows for a longer preservation of the filtered sample. The new method described in this paper was tested along an entire river-seawater gradient of the Aulne Estuary (Brittany, France) to assess its capability in terms of determining these natural organic compounds in various surface waters.