Abstract The ability to analyze samples with disparate levels of analyte and matrix ions is among the important benefits defining the practical utility of modern capillary electrophoresis. To compensate for the sensitivity limitations regarding trace-level inorganic anions, a number of on-line approaches that should offer an improved S/N ratio in direct UV detection were examined. The novel use of reversed pre-electrophoresis (at the applied voltage opposite to the separation voltage) made it possible to efficiently remove the most part of high chloride levels from the sample and hence to lower the background signal and to inject increased quantities of fast analyte anions. Specifically, by taking these advantages the sensitivity response of iodide was improved by a factor of 5 over normal CE mode. Using isotachophoretic sample stacking, a two-fold increase in detectability was obtained for moderately mobile anions, nitrate and nitrite, that corresponds to the minimum detectable concentrations close to their natural occurrences in seawater. Furthermore, field-amplified sample injection at increased electrolyte-to-sample matrix concentration ratios enabled the maximum S/N enhancement, with detection limits at the level of 10 −6 M and lower in the presence of ≥5·10 4-fold molar excess of chloride.