Ab initio and classical molecular dynamics simulations show that water can flow through graphdiyne—an experimentally fabricated graphene-like membrane with highly dense (2.4 × 10¹⁸ pores/m²), uniformly ordered, subnanometer pores (incircle diameter 0.57 nm and van der Waals area 0.06 nm²). Water transports through subnanopores via a chemical-reaction-like activated process. The activated water flow can be precisely controlled through fine adjustment of working temperature and pressure. In contrast to a linear dependence on pressure for conventional membranes, here pressure directly modulates the activation energy, leading to a nonlinear water flow as a function of pressure. Consequently, high flux (1.6 L/Day/cm²/MPa) with 100% salt rejection efficiency is achieved at reasonable temperatures and pressures, suggesting graphdiyne can serve as an excellent membrane for water desalination. We further show that to get through subnanopores water molecule must break redundant hydrogen bonds to form a two-hydrogen-bond transient structure. Our study unveils the principles and atomistic mechanism for water transport through pores in ultimate size limit, and offers new insights on water permeation through nanochannels, design of molecule sieving and nanofluidic manipulation.