Membrane ultrafiltration is an extensively used technique for water purification and hence understanding the water flow confined in nanochannels is of vital importance. As a key parameter, water permeability has been the focus of fundamental researches and technical applications. However, water permeability in sub‐100 nm regime is not yet well understood as evidenced by the previously published data which are divergent from theory. Here, the precise determination of water permeabilities of sub‐100 nm nanochannels is reported. This is achieved by the proposed innovative pore diameter‐calibration method with excellent accuracy through replicating the pore geometry, and using the nanoporous ion track‐etched membrane as a model system which features well‐defined, cylindrical, straight, and equally sized nanochannels. Thanks to this accurate calibration method, the measured permeabilities show a remarkably improved precision as compared to the previously reported data. In addition, the measured permeabilities of the ultrafiltration channels are lower than the theoretical predictions. The discrepancy is explained under the framework of the wettability effect. It is expected that the work will shed light on a controversy over a decrease or increase in water permeability of ultrafiltration membranes and also guide the design of ultrafiltration membranes for water purification and separation applications.