We present molecular dynamics simulation of molecules transporting through carbon nanotubes for applications in engineered flow channels, focusing on the dynamics of molecules spontaneously inserted into the nanotube channel in aqueous environment. The molecules studied include a C60 molecule, a finite segment of carbon nanotube with smaller diameter, and single/double- stranded DNA molecules. We show that in the absence of water solvation, the van der Waals interaction between the molecule and the nanotube wall can induce a rapid spontaneous encapsulation of the molecule inside the nanotube channel. The encapsulation process is strongly impeded for nanotube dissolved in water due to the competition between the van der Waals, hydrophobic and hydrogen bonding interactions in the nanotube/water/molecule complex. Water adsorption inside the nanotube channel plays an important role in determining the dynamics of the spontaneous insertion process.