Nearly frictionless water transport makes carbon nanotubes promising materials for use as conduits in nanofluidic applications. Here, we conduct molecular dynamics simulations of water flow within amorphous silica nanopores coated by a (39,39) single-walled carbon nanotube (SWCNT). Our atomistic models describe the interaction between water and pore walls based on two possible scenarios, translucency and opacity to wetting of a SWCNT. Simulation results indicate that the SWCNT coating enhances water flow through silica pores ca. 10 times compared to predictions from the classical Hagen–Poiseuille relation. By varying the strength of the water–pore interaction, we study the relationship between surface wettability and hydrodynamic slippage. We observe an increase in the slip length for higher values of water contact angle. Moreover, cases with SWCNT opacity and translucency to wetting display a substantial difference in the computed slippage, showing that the water contact angle is not the only factor that determines the slip boundary condition under nanoconfinement. We attribute this disparity to the corrugation of the potential energy landscape at the inner pore wall. The present study provides a theoretical framework for the use of carbon nanotube-based coatings in designing more efficient nanofluidic conduits.