Biological pores regulate the cellular traffic of a large variety of solutes, often with high selectivity and fast flow rates. These pores share several common structural features: the inner surface of the pore is frequently lined with hydrophobic residues, and the selectivity filter regions often contain charged functional groups. Hydrophobic, narrow-diameter carbon nanotubes can provide a simplified model of membrane channels by reproducing these critical features in a simpler and more robust platform. Previous studies demonstrated that carbon nanotube pores can support a water flux comparable to natural aquaporin channels. Here, we investigate ion transport through these pores using a sub-2-nm, aligned carbon nanotube membrane nanofluidic platform. To mimic the charged groups at the selectivity region, we introduce negatively charged groups at the opening of the carbon nanotubes by plasma treatment. Pressure-driven filtration experiments, coupled with capillary electrophoresis analysis of the permeate and feed, are used to quantify ion exclusion in these membranes as a function of solution ionic strength, pH, and ion valence. We show that carbon nanotube membranes exhibit significant ion exclusion that can be as high as 98% under certain conditions. Our results strongly support a Donnan-type rejection mechanism, dominated by electrostatic interactions between fixed membrane charges and mobile ions, whereas steric and hydrodynamic effects appear to be less important.