A primary obstacle in understanding the fate and transport of the toxic radionuclide 129I (a thyroid seeker) is an accurate method to distinguish it from the stable isotope, 127I, and to quantify the various species at environmentally relevant concentrations (~10−8M). A pH-dependent solvent extraction and combustion method was paired with accelerator mass spectrometry (AMS) to measure ambient levels of 129I/127I isotope ratios and iodine speciation (iodide (I−), iodate (IO3−), and organo-I (OI)) in aquatic systems. The method exhibited an overall uncertainty of 10% or less for I− and IO3−, and less than 30% for OI species concentrations and enabled 129I measurements as low as 0.001Bq/L (1Bq/L=10−13M). The method was used to analyze groundwater from the Savannah River Site (SRS), South Carolina, USA, along a pH, redox potential (Eh), and organic carbon gradient (8–60μM DOC). The data confirmed that the 129I/127I ratios and species distribution were strongly pH dependent and varied in a systematic manner from the strongly acidic source. While 129I speciation in plume samples containing total I concentrations >1.7Bq/L was similar whether measured by AMS or GC–MS ([I−]≫[IO3−]=[OI]), AMS enabled 129I speciation measurements at much lower concentrations than what was possible with GC–MS. AMS analyses demonstrated that groundwater samples minimally impacted by the plume were still orders of magnitude higher than ambient 129I concentrations typically found elsewhere in the USA groundwaters and rivers. This is likely due to past atmospheric releases of volatile 129I species by SRS nuclear reprocessing facilities near the study site. Furthermore, the results confirmed the existence of 129I not only as I−, but also as OI and IO3− species.