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The separation and determination of a mixture of chloro- and methylthiotriazines in water samples by both micellar electrokinetic capillary chromatography (MEKC) and nonaqueous capillary zone electrophoresis (NA-CZE) were compared. The characteristics of both methods proved to be very similar in terms of separation efficiency and analysis times, but application of these methods for the analysis of triazines in natural waters, with a prior preconcentration step, revealed significant differences. A preconcentration step by solid-phase extraction (SPE) with Oasis HLB cartridges was accomplished for the determination of triazines at sub-ppb levels in drinking and river waters; when NA-CZE was used after this SPE step, electropherograms with fewer interferences and more stable baselines were obtained than when separation was carried out using MEKC. Another aspect related to the application to real samples was the lack of precision encountered upon evaluating the electrophoretic signals generated when using SPE coupled with NA-CZE. Here, we demonstrate the importance of choosing an appropriate internal standard for analyte quantification. It is recommended that a triazine belonging to the same family as that of the triazine to be determined should be used as internal standard.