The rejection of particles with different charges and sizes, ranging from a few Ångstroms to tens of nanometers, is key to a wide range of industrial applications, from wastewater treatment to product purification in biotech processes. Carbon nanotubes (CNTs) have long held the promise to revolutionize filtration, with orders of magnitude higher fluxes compared to commercial membranes. CNTs, however, can only reject particles and ions wider than their internal diameter. In this work, the fabrication of aligned boron nitride nanotube (BNNT) membranes capable of rejecting nanoparticles smaller than their internal diameter is reported for the first time. This is due to a mechanism of charge-based rejection in addition to the size-based one, enabled by the BNNTs surface structure and chemistry and elucidated here using high fidelity molecular dynamics and Brownian dynamics simulations. This results in ∼40% higher rejection of the same particles by BNNT membranes than CNT ones with comparable nanotube diameter. Furthermore, since permeance is proportional to the square of the nanotubes’ diameter, using BNNT membranes with ∼30% larger nanotube diameter than a CNT membrane with comparable rejection would result in up to 70% higher permeance. These results open the way to the design of more effective nanotube membranes, capable of high particle rejection and, at the same time, high water permeance.