Simulations and measurements have established that water moves through carbon nanotubes with exceptionally high rates due to nearly frictionless interfaces1–4. These observations have stimulated interest in nanotube-based membranes for applications that range from desalination to nano-filtration and energy harvesting5–10, yet the exact water transport mechanisms inside the nanotubes and at the water-carbon interface continue to be controversially discussed11,12 because existing theories fail to provide a satisfying explanation for the limited number of experimental results available to date13. This is because even though controlled and systematic studies have explored transport through individual nanotubes8,9,14–7, none has met the considerable technical challenge of unambiguously measuring the permeability of a single nanotube11. Here we show that the pressure-driven flow rate across individual nanotubes can be determined with unprecedented sensitivity and without dyes from the hydrodynamics of water jets as they emerge from single nanotubes into a surrounding fluid. Our measurements reveal unexpectedly large and radius-dependent surface slippage in carbon nanotubes (CNT), and no slippage in boron-nitride nanotubes (BNNT) that are crystallographically similar to CNTs but differ electronically. This pronounced contrast between the two systems must originate from subtle differences in atomic-scale details of their solid-liquid interfaces, strikingly illustrating that nanofluidics is the frontier where the continuum picture of fluid mechanics confronts the atomic nature of matter.