We describe capillary zone electrophoresis (CZE) with transient isotachophoresis (ITP) for the determination of low concentrations of nitrite and nitrate ions in seawater. Bromide-free artificial seawater was adopted as background electrolyte (BGE) to eliminate the interference of high concentrations of salts in seawater. To reverse the electroosmotic flow (EOF), 3 mM cetyltrimethylammonium chloride (CTAC) was added to the BGE. High concentrations of chlorate were added to sample solutions as the terminating ion to generate the ITP process before the CZE separation. In general, the stacking effect increased with increasing amounts of chlorate injected into the capillary. The limits of detection (LODs) for nitrite and nitrate were 0.063 and 0.033 mg/L when the chlorate concentration was 600 and 200 mM, respectively; these were half of those obtained by CZE without the transient ITP. The LODs were obtained at a signal to noise ratio (S/N) of 3. The relative standard deviations (RSD, n = 10) of the peak areas for these ions were 3.2 and 2.9%. The RSDs of peak heights for these ions were 1.6 and 2.1%. The RSDs of migration times for these ions were 0.67 and 0.46%.