A contactless conductometric detection (CCD) system for capillary electrophoresis (CE) with a flexible detection cell was applied for the simultaneous determination of small anions and/or cations in rain, surface and drainage water samples. The applied frequency, the amplitude of the input signal, the electrolyte conductivity and electrode distance were found to be the most significant factors affecting the detection sensitivity. 2-(N-Morpholino)ethanesulfonic acid/histidine-based (MES/His) electrolytes were used for direct conductivity detection of anions and cations, while ammonium acetate was selected for indirect conductivity determination of alkylammonium salts. For the simultaneous separation procedure, involving dual-opposite end injection, an electrolyte consisting of 20 mM MES/His, 1.5 mM 18-crown-6 and 20 microM cetyltrimethylammonium bromide provided baseline separation of 13 anions and cations in less than 6 min. The detection limits achieved were 7-30 micrograms/l for direct conductometric detection of various common inorganic cations and anions, excluding F- (62 micrograms/l) and H2PO4- (250 micrograms/l), and 35-178 micrograms/l for indirect conductometric detection of alkyl ammonium cations. The developed electrophoretic method with conductometric detection was compared to ion chromatography.