Recently, organic nanostructures have attracted much attention, and amongst them peptide nanotubes are of interest in many fields of application including medicine and nanobiotechnology. Peptide nanotubes are formed by self-assembly of cyclic peptides with alternating L- and D-amino acids. Due to their biodegradability, flexible design and easy synthesis, many applications have been proposed such as artificial transmembrane ion channels, templates for nanoparticles, mimicking pore structures, nanoscale testing tubes, biosensors and carriers for targeted drug delivery. The mechanisms of an ion, a water molecule and an ion–water cluster entering into a peptide nanotube of structure cyclo[(-D-Ala-L-Ala-)(Formula presented.)] are explored here. In particular, the Lennard-Jones potential and a continuum approach are employed to determine three entering mechanisms: (i) through the tube open end, (ii) through a region between each cyclic peptide ring and (iii) around the edge of the tube open end. The results show that while entering the nanotube by method (i) is possible, an ion or a molecule requires initial energy to overcome an energetic barrier to be able to enter the nanotube through positions (ii) and (iii). Due to its simple structure, the D-, L-Ala cyclopeptide nanotube is chosen in this model; however, it can be easily extended to include more complicated nanotubes.