A transient micellar phase extractor using CTAB was described for the online sample concentration of various anionic analytes (drugs and herbicides) in CE. Stacking and separation was performed at neutral pH in coelectroosmotic flow in a hexadimethrine bromide coated fused-silica capillary. A micellar plug (e.g. 10 mM CTAB) was injected prior to hydrodynamic injection of the analytes prepared in aqueous organic solvent (e.g. with 30% ACN). In the presence of an electric field, the micelles interacted with the anions inside the capillary. This was followed by selective analyte focusing via the mechanism of micelle to solvent stacking. The micelles acted as transient extractor because the stacking ends when the injected micelles completely migrated through the boundary between the sample and micellar plug. Fundamental studies were performed (effect of surfactant concentration, etc.) and the technique yielded 13- to 30-fold improvements in peak height. A stacking CE method in conjunction with liquid–liquid extraction was also tested for the detection of the herbicides fenoprop and mecoprop in fortified drinking water at analyte concentration levels relevant to Australian Drinking Water Guidelines.