Collagen is the most abundant protein in higher vertebrates. Despite collagen repetitive sequence, several aspects of its structure and stability are controversial. Here we performed molecular dynamics simulations to analyze triple helix hydration in regions characterized by different imino/aminoacid contents. Data emerged from MD simulations show that (a) MD simulations can reliably reproduce the hydration sites identified experimentally, (b) water molecules bound to regions with a different amino/iminoacid content exhibit diversified residence times, and (c) in the aminoacid-rich region the binding of water molecules is strongly influenced by the local sequence of the peptide. MD results also suggest that, in aminoacid-rich regions, the stabilizing effects of Arg and Hyp residues on collagen triple helix also depend on water-mediated interactions. On this basis, we propose that the mechanism of triple helix stabilization is sequence-dependent.