The separation of empty and water-filled laser ablation and electric arc synthesized nanotubes is reported. Centrifugation of these large-diameter nanotubes dispersed with sodium deoxycholate using specific conditions produces isolated bands of empty and water-filled nanotubes without significant diameter selection. This separation is shown to be consistent across multiple nanotube populations dispersed from different source soots. Detailed spectroscopic characterization of the resulting empty and filled fractions reveals that water filling leads to systematic changes to the optical and vibrational properties. Furthermore, sequential separation of the resolved fractions using cosurfactants and density gradient ultracentrifugation reveals that water filling strongly influences the optimal conditions for metallic and semiconducting separation.