We use molecular dynamics simulations to study the diffusion of water inside deformed carbon nanotubes with different degrees of deformation at 300 K. We found that the number of hydrogen bonds that water forms depends on nanotube topology, leading to enhancement or suppression of water diffusion. The simulation results reveal that more realistic nanotubes should be considered to understand the confined water diffusion behavior, at least for the narrowest nanotubes, when the interaction between water molecules and carbon atoms is relevant.