The ultra-low friction observed between water and carbon nanotubes has been extensively reported recently. In this study, we delve into the factors influencing the liquid–solid friction, including surface properties such as surface wettability and roughness of carbon nanotubes, as well as the driving forces involving temperature gradient and pressure drop. Utilizing non-equilibrium molecular dynamics simulations on carbon nanotube models with a diameter of ~1 nm, we observe a significant increase in water flux within a specific range of wettability, independent of roughness. This range is expected to shift to smaller values with increased pressure drop and temperature gradient. Both the mechanical transport coefficient and the thermo-osmosis coefficient exhibit a negative correlation with wettability, and roughness further decreases these coefficients. Through this work, we provide insights into the effects of surface properties on fluid transport through nanopores, contributing valuable information for the optimization of high-performance membrane processes.