In capillary electrophoresis (CE) analysis of small inorganic anions, the ability to control the electroosmotic flow (EOF) and the ability to alter the electrophoretic mobility of the ions are essential to improve resolution and separation speed. In this work, a CE method for separation of small inorganic anions using indirect detection in mixed methanol/water buffers is presented. The suitability of different UV absorbing probes commonly used for indirect detection including chromate, iodide, phthalate, benzoate, trimellitate, and pyromellitate, in mixed methanol/water buffers is examined. The effect of the electrolyte buffer system, including the pH, buffer concentration and the organic solvent on the electrophoretic mobility of the probes and analytes are also investigated. The EOF was reversed using cationic surfactant, cetyltrimethylammonium bromide (CTAB) so ions were separated under co-EOF mode. The organic solvent alters the electrophoretic mobility of the probes and the analytes differently and hence choice of the appropriate probe is essential to achieve high degree of detection sensitivity. Separations of six anions in less than 2.5 min were accomplished in buffers containing up to 30% MeOH. Adjustment of the methanol content helps to improve the selectivity and resolution of inorganic anions. Limit of detection, reproducibility and application of the method for quantification of anions in water samples will also be discussed.