We investigate here water flow passing a single-walled carbon nanotube (CNT), through analysis based on combined atomistic and continuum mechanics simulations. The relation between drag coefficient C(D) and Reynolds number Re is obtained for a wide range of flow speed u from 5 to 600 m/s. The results suggest that Stokes law for creep flow works well for small Reynolds numbers up to 0.1 (u ≈ 100 m/s), and indicates a linear dependence between drag force and flow velocity. Significant deviation is observed at elevated Re values, which is discussed by considering the interfacial slippage, reduction of viscosity due to friction-induced local heating, and flow-induced structural vibration. We find that interfacial slippage has a limited contribution to the reduction of the resistance, and excitations of low-frequency vibration modes in the carbon nanotube play an important role in energy transfer between water and carbon nanotubes, especially at high flow speeds where drastic enhancement of the carbon nanotube vibration is observed. The results reported here reveal nanoscale fluid-structure interacting mechanisms, and lay the ground for rational design of nanofluidics and nanoelectromechanical devices operating in a fluidic environment.