We perform total-energy electronic-structure calculations of a water molecule inside a (7, 7) carbon nanotube/ boron nitride nanotube (CNT/BNNT) heterojunction. The van der Waals interaction is also considered in this study. We find that the equilibrium distance between the water molecule and the wall of the CNT (BNNT) is approximate to 3.3 angstrom, and the encapsulation energy is 0.22 eV (0.25 eV). The energy profile along the tube axis exhibits a dramatic change in the vicinity of the heterojunction. A speed change of water flow is expected to occur near the heterojunction. Such information would provide valuable insight in nanostructure design for nanofluidics.