An on-line tagging of target species is simulated using the finite element method. A numerical model of an electrochemical EC(2X)E mechanism in a flow channel cell has been developed, corresponding to the electrochemical generation of a probe and the subsequent homogeneous reaction with the target. The kinetic and convective aspects are validated on short electrode geometries before taking into account the depletion of the target species. The model is then assessed according to previous experimental results on the on-line tagging of proteins. The occurrence and the efficiency of the on-line tagging are studied for both pressure-driven and electroosmotic flows. The involved phenomena including kinetic aspects are described in detail. Finally, optimal conditions for an effective quantitative tagging are discussed.