In this paper, we present an online coupling of gel electrophoresis (GE) and inductively coupled plasma-mass spectrometry (ICP-MS) for the determination of iodine species (iodide and iodate) in liquid (seawater) and aerosol samples. For the first time, this approach is applied to the analysis of small molecules, and initial systematic investigations revealed that the migration behavior as well as the detection sensitivity strongly depends on the matrix (e.g., high concentrations of chloride). These effects could consequently affect the accuracy of analytical results, so that they need to be considered for the analysis of real samples. The technique used for quantification is species-specific isotope dilution analysis (ssIDA), which is a matrix-independent calibration method under certain conditions. We demonstrate that the use of 129I-enriched iodide and iodate allows the correction of the impact of the matrix on both, the electrophoretic migration and the detection sensitivity of the ICP-MS. After optimization, this coupling offers a novel and alternative method in the analysis of iodine compounds in various matrices. Here, we demonstrate the analytical capability of the technique for the chemical characterization of marine aerosols. The results show the presence of iodide and iodate at the ng m(-3) and sub-ng m(-3) level in the investigated aerosol samples, which were taken at the coastal research station in Mace Head, Ireland. These results are in good agreement with other recent studies, which demonstrated that the iodine chemistry in the marine atmosphere is only poorly understood. In addition to iodide and iodate, another iodine compound could be separated and detected in certain samples with high total iodine concentrations and was identified as elemental iodine, probably in form of triiodide, by peak matching. However, it may arise from an artifact during sample preparation.