Four different running capillary zone electrophoresis (CZE) buffers suitable for an indirect photometric detection were studied. The influence of several variables (buffer pH, concentration of electrophoretic flow modifiers, capillary diameter and applied voltage) on determination of chloride, sulphate, nitrate, fluoride, and phosphate was tested for each buffer. All the tested buffers proved to be suitable for the determination. PMA‐TEMED running buffer (pyromellitic acid‐tetramethylethylendiamine) was finally adopted for further investigation. The optimized PMA‐TEMED method was tested on several hundred samples of atmospheric deposition taken in the Czech Soil Monitoring Programme and lyzimetric waters from experimental stations. For analysis of water soil extracts six different soils from international and national soil proficiency tests were analyzed. Analysis of the water soil extracts was more complicated than analysis of atmospheric deposition because more unknown peaks were detected. Concentration of phosphorus in the water soil extracts was usually lower than the detection limit of the method. The proposed method proved to be suitable for determination of chloride, sulphate, nitrate, and fluoride in atmospheric deposition, lyzimetric waters, and soil water extracts.