The movement of nanoparticles across cell membranes in a controlled manner is important for developing applications related to filtration, penetration, and biological systems. Here, the tunable transport of metal nanoparticle suspensions with well-defined particle sizes and surface groups through a ≈1 mm-thick porous carbon nanotube sponge filter is reported. Au particles with a relatively large diameter (40 nm) alone are easily trapped by the nanotube sponge even in a dilute water flow, but they can quickly pass through the sponges by the addition of much smaller particles (4 nm) to the suspension. A mechanistic study shows that the dominating interaction mode between Au particles and the sponge is physical trapping within the nanotube networks rather than Coulomb attraction. In the nanoparticle mixture, surface groups on the small particles tend to form hydrogen bonds with groups on large particles, thereby increasing interparticle distances, and preventing formation of severe agglomerates; large particles can therefore move across interconnected nanotubes more smoothly. It might be possible to switch the transport of many different nanoparticles across porous media on and off by adding or removing smaller particles of the same type.