The influence of varying experimental conditions on the mobilities of inorganic and organic anions in ion chromatography-capillary electrophoresis (IC-CE) was studied. A theoretical model derived from both IC and CE was used to explain the influence on analyte mobility caused by varying the concentration of polymer and increasing the salt concentration in the background electrolyte. The influence of the type of competing ion was also accounted for by including the analyte selectivity coefficient in the model equation. The validity of the model was shown using electrolyte systems containing four different competing anions, with correlation between experimental and mobilities predicted being excellent (r(2) > 0.98) for all systems. Selectivity coefficients determined via nonlinear regression enabled quantitative comparisons of different competing ion strength, with the eluting strength increasing in the order of fluoride, acetate, chloride, and sulfate. Optimization of the polymer and eluent concentration was performed for all electrolyte systems using the normalized resolution product optimization criterion, requiring only seven experiments to obtain the optimum conditions for complete separation. The minimum resolution criterion was used to optimize the fluoride system which gave a different separation selectivity from both CE and IC.