Capillary electrophoresis was used for separation and quantitation of several inorganic anions in the drainage and surface water samples from the region with extensive use of fertilisers. Baseline separation of 13 small anions including nitrite and nitrate up to the concentrations of 100 mg/l was achieved in less than 5 min. The electrolyte consisted of 3 mM K2CrO4, 30 microM cetyltrimethylammonium bromide and 3 mM boric acid at pH 8. The method yielded precisions of 1.8-7.2% (RSD, n = 10) and detection limits from 4 micrograms/l (Cl-) up to 500 micrograms/l (citrate). The results of the CE method were compared to ion chromatography using water-acetonitrile (86:14) at pH 8.6 adjusted with NaOH as the mobile phase and consistent results were obtained.