Here, we combined lipid nanovesicles (ethosomes, liposomes) as the drug carrier systems with two physical methods (electroporation, sonoporation) to enhance transdermal delivery of a hydrophilic model molecule, calcein. First, using different formulations, ethosomes greatly enhanced calcein permeation by passive diffusion compared to liposomes and calcein in buffer, which is most likely due to a synergism between the ethanol action on the stratum corneum lipids and the penetration of the elastic vesicles. Liposomes permeated poorly through the skin and, as also suggested by other authors, seem to remain confined to the outer layers of the skin. By creating localized effects, liposomes would be better suited to topical dermal delivery than transdermal delivery. Using sonoporation as the physical enhancement method, sonication (5 min) showed improvement over passive diffusion; however, only for the ethosome formulation, and not for solution and liposomes. Similarly, electroporation greatly enhanced delivery of calcein, which was again more pronounced for ethosomes than liposomes and calcein in buffer. Finally, three different transdermal delivery enhancement methods were coupled, using ethosomes as carriers, along with both electroporation and sonoporation, to investigate the potential for synergistic effects. However, these combinations failed to achieve not only synergistic effects, but also additive effects. Nevertheless, combination of the ethosome formulation of calcein with either of electroporation or sonoporation achieves significant enhancement of transdermal molecular delivery being safe for potential clinical use.