Transport of ions and molecules through nanochannels has been of interest due to the desire to understand the activity of biological ion channels and the prospect of exploiting the property in biomedical and chemical applications, such as molecular delivery and sensing. Nanochannels with critical dimensions comparable to Debye length exhibit surface charge-governed ion transport which is not accessible in microfluidic devices. To look into this unique phenomenon, we present our experimental and theoretical studies of the electrokinetic ion transport through sub-20 nm thick nanochannels.First we demonstrated ion current rectification in homogeneous silica nanochannels with ion concentration gradients. Depending on the polarity of the applied electric field, the uneven ion flux from the two ends can accumulate or deplete the ions in the nanochannel and results in asymmetric ionic conductances. Such rectifying effect was found to stem from the asymmetric cation-anion ratios at two ends of channel. The model elucidates the essential physics for the similar rectification effects reported previously in conical nanopores and nanofluidic diodes. Prior to this unified model, the rectifying effect in different nanofluidic devices were treated on the individual bases.In addition, we developed heterogeneous nanofluidic devices for the control of ion flow with well-defined surface charge distribution by patterning alumina and silica surfaces. Nanofluidic diodes were successfully fabricated by this method and demonstrated rectifying factor greater than 300 which is the highest reported to date. It was also found the different surface charge polarity inside and outside the nanochannel works as a parasitic diode and can affect ion transport. The finding suggests that the nano-/microchannel interface be taken into account in interpreting the physics of ion transport in nanochannels. Apart from electrokinetic transport in nanochannels, we demonstrated a directional, active molecule transport by utilizing the kinesin motor proteins immobilized in the opened nanochannels to propel microtubules along the nanochannels. Due to the physical confinement of the nanochannels, microtubules can glide over a long distance without detaching from the surface. This demonstration opens up the possibility of utilizing the biological molecules and artificial nanostructures to carry out several desired functions, e.g. chemical delivery or molecule concentration.