The Republic of Bulgaria regulates the quality of surface waters for drinking and domestic purposes, monitoring anions like F-, Cl-, Br-, I-, BrO3-, NO2-, NO3-, SO42-, PO43-, and SCN-. The presence of NO3- and NO2- in water is undesirable, as they have a harmful effect on human health. It is also well known that CN- as opposed to SCN- has acute toxic and lethal effects on living organisms including humans. In the present study, an instrumental method was developed and optimized for the separation and quantification of inorganic anions in surface and drinking water using ion chromatography. The analytical characteristics of the proposed instrumental method were determined. The oxidation of CN- to OCN- was investigated, and the optimal experimental conditions for the oxidation were established. The achieved low LOD and LOQ of the analyzed inorganic anions allows their detection and quantification in surface and drinking waters. The applicability of the proposed chromatographic method was determined in the analysis of surface and bottled waters. The analyzed anions in bottled waters were close to the label's values, only one spring water showed significant deviations.