In this study, we used non-equilibrium molecular dynamics to study the transport of water through deformed (6,6) Carbon Nanotubes (CNTs) and Boron Nitride Nanotubes (BNNTs). The results were then compared with that of the perfect nanotubes. The main aim of this study was to get a better insight into the deformation effect on water transport through nanotubes rather than directly comparing the CNTs and BNNTs. As the diameters of both types of nanotubes differ from each other for the same chiral value, they are not directly comparable. We carried out our study on deformations such as screw distortion, XY-distortion, and Z-distortion. XY-distortion of value 2 shows a change from single-file water transport to near-Fickian diffusion. The XY-distortions of higher value shows a notable negative effect on water transport when their distortion values get larger. These suggest that the degree of deformation plays a crucial role in water transport through deformed nanotubes. The Z-distortion of 2 showed discontinuous single-file chain formation inside the nanotubes. Similar phenomena are observed in both nanotubes, irrespective of their type, while the magnitudes of their effects vary.