Recently developed analytical techniques allowed for the detection of a range of dissolved arsenic-sulphur species in sulphur-rich environments. These so called thioarsenates are unstable, however, and can degrade upon handling and storage. An experiment evaluating the effect of exposure to air on arsenic and sulphur-enriched geothermal waters demonstrated a near to complete loss of thioarsenate species to arsenite or arsenate during short oxidation times. In contrast, thioarsenic standards were stable for the duration of analysis in spite of exposure to air. For samples containing thio-methylated arsenic species, the extent of oxidation varied for different methylated arsenic species. This study recommends flash freezing of samples in liquid nitrogen immediately after recovery and further storage under anaerobic conditions at − 80 °C. A second experiment to test the efficiencies of different HPLC columns for separating arsenic species resulted in the preference for an IonPac column with NaOH as the mobile phase when analysing arsenic thioanions, over the commonly used PEEK PRP-X100 anion exchange and Atlantis C18 reverse phase column with ammonium phosphate mobile phases. Distinct separation of thio-methylated arsenic species with the IonPac column, however, was not successful potentially due to matrix components. Acceptable detection, separation and quantification of thio-methylated arsenic species were only achieved with the Atlantis C18 column. This study shows that preservation and analysis of samples is matrix dependent, which holds important implications for efforts to interpret arsenic speciation in geothermal waters, especially those of low pH (2–3), low oxygen (≤ 49% saturation), low iron (≤ 5 mg L − 1) and high sulphur concentrations (≥ 91 mg L − 1).