Metal toxicity is not related to the total metal ion concentration, but to those of some specific Cu(II) species. The Permeation Liquid Membrane technique is based on the carrier-mediated transport of the test metal across a hydrophobic membrane and enables discrimination between various trace metal species in solution. The present work shows how the labile and inert Cu(II) complexes can be determined selectively, by varying the flow-rate of the test solution, in a flow-through cell. A mathematical model of metal flux through the PLM, based on diffusion-limited transport under steady-state conditions, is described. The model and the performance of the technique were studied in well-defined synthetic solutions containing simple organic hydrophilic ligands forming either inert (nitrilotriacetic acid), or labile complexes with Cu(II) (tartaric acid, malonic acid). The results were compared with theoretical predictions of thermodynamic species distribution in solution. Uncertainties on stability constants for copper speciation calculation were taken into account. The detection limits of the device are discussed. This work demonstrates that the flow-through cell is a reliable tool for copper speciation measurements in natural waters.