Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) facilitates determination of both the kinetic constants (k(off)) and the equilibrium constants (K(d)) of complex dissociation from a single experiment. A typical NECEEM electropherogram consists of two peaks and an "exponential bridge" between them, smoothly merging into the peaks. The values of k(off) and K(d) are usually calculated with simple algebraic formulas, by utilizing the areas of the peaks and the bridge. Accurate determination of the two constants requires accurate positioning of the two boundaries separating the bridge from the peaks. Here, we propose a more systematic method for the determination of boundaries between the peaks and the bridge. The method involves a simple geometrical analysis of a NECEEM electropherogram based on an assumption of symmetry in ordinary electrophoretic peaks. To test the method, we (i) constructed a series of computer-simulated NECEEM electropherograms, (ii) determined the two boundaries with our method, and (iii) calculated the values of k(off) and K(d). We found that the deviation of the calculated values from those used to simulate the electropherograms did not exceed 15% for k(off) and 25% for K(d), as long as the peaks and the bridge were visually identifiable. We finally applied the method to the determination of K(d) and k(off) values for the interaction between AlkB protein and its DNA aptamer. The developed method for rational boundary determination in NECEEM will facilitate accurate data analysis in a simple and efficient manner.