Molecular transport through nanoporous nuclear-track-etched membranes was investigated with fluorescent probes by manipulating applied electric field polarity, pore size, membrane surface functionality, pH, and the ionic strength. Three forces contribute to analyte transport through membranes: ion migration, electroosmosis, and diffusion. Diffusion dominates under field-free conditions with surface hydrophobicity controlling solvent access to the nanochannels and hence the magnitude of transport by diffusion. In low ionic strength solutions (mu similar to 10 mM), electroosmosis dominates transport when the membranes are biased, and the charge state of the surface determines the direction of flow. At high ionic strength (mu similar to 1 M), ion migration dominates in hydrophobic membranes, and diffusion is controlling in hydrophilic membranes. The magnitude and polarity of the interior surface charge is controlled by surface functionality and displays the largest impact on molecular transport. The analyte can migrate in opposite directions under the same applied electric field by modifying either membrane surface charge or solution ionic strength. Transport can be fine-tuned by adjusting pH under low ionic strength conditions in either type of membrane. Increasing the surface charge density, sigma (s) enhances the mobile counterion. concentration, increasing the electroosmotically driven flux. Comparisons of behavior under different conditions are understood by reference to the product, kappa alpha, of the inverse Debye length, kappa, and the pore diameter, alpha.