This paper deals with unwanted effects of carbonate in capillary zone electrophoretic analyses of anions in alkaline BGEs with indirect UV absorption and conductivity detection. Computer simulations and experimental study of selected model systems have shown that carbon dioxide absorbed from air into BGEs and samples induce important electrophoretic effects like formation of new additional zones and/or boundaries that may further induce strong and pronounced temporary changes in the migration of analytes. Examples are reduction of the pH of alkaline BGEs around pH 11 by up to 1 unit or formation of a pronounced detectable carbon dioxide peak comparable with peaks of analytes at 1 mM level. The higher the pH of the BGE, the stronger these effects and the broader their spectrum, involving (i) changes of effective mobilities and selectivity due to changes in pH of the BGE, (ii) occurrence of additional system zones appearing in form of peaks, dips or more complex disturbances in the detection signal, (iii) temporary interactions with the sample components and subsequent modification of the separation process and of its result. This paper reveals all these effects and brings the knowledge necessary to prevent problems with qualitative and quantitative evaluation of the analysis results.