This paper deals with the determination of the more complex phosphate anion by capillary electrophoresis using indirect UV detection. First, the pH of the running electrolyte influences both the migration time and the response of the phosphate anion. Both effects could be explained well by taking into account phosphorus speciation in solution. In addition, the experimental method has been applied to three different sets of natural water systems; (i) groundwater, (ii) surface water and (iii) stemflow samples. The migration time behaviour of phosphate was different for the three sample sets and, hence, difficulties arise with respect to a clear and unique identification of the compound. Deviations herein could be minimized by applying a correction method for migration time drift. Concentrations of phosphate could be quantified in most samples and were confirmed by a colorimetric method. Average recoveries of additions of phosphate to groundwater, surface water and stemflow samples were 105, 83 and 103%, respectively. For one stemflow sample, quantitative recovery of phosphate was possible only by changing the pH of the running electrolyte solution. The latter observation might be very useful in setting up speciation-related measurement methods.