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The effectiveness of nanoparticle-based functional devices depends strongly on the surface morphology and area of the support. An emerging powerful approach of increasing the available surface area without decreasing strength or increasing bulk is to attach arrays of suitable nanotubes on the surface, and to attach the necessary nanoparticles to them. Earlier publications by this team have shown that carpet-like arrays of carbon nanotubes (CNTs) can be successfully grown on a variety of larger carbon substrates such as graphite, foams and fabric, which offer hierarchical multiscale supporting architecture suitable for the attachment of silver nanoparticles (AgNPs). A limiting factor of pure CNT arrays in fluid-based applications is their hydrophobicity, which can reduce the percolation of an aqueous medium through individual nanotubes. Previous studies have demonstrated that the treatment of CNT carpets with dry (oxygen) plasma can induce reversible wettability, and treatment with wet (sol–gel) coating can impart permanent wettability. In this paper, we report the influence of such treatments on the attachment of AgNPs, and their effectiveness in water disinfection treatments. Both types of hydrophilic surface treatment show an increase in silver loading on the CNT carpets. Oxygen-plasma treated surfaces (O-CNT) show fine and densely packed AgNPs, whereas silica-coated nanotubes (silica-CNT) show uneven clusters of AgNPs. However, O-CNT surfaces lose their hydrophilicity during AgNP deposition, whereas silica-CNT surfaces remain hydrophilic. This difference significantly impacts the antibacterial effectiveness of these materials, as tested in simulated water containing Gram negative Escherichia coli (E. coli, JM109). AgNPs on silica-coated CNT substrates showed significantly higher reduction rates of E. coli compared to AgNPs on plasma-treated CNT substrates, despite the finer and better dispersed AgNP distribution in the latter. These results provide important insights into different aspects of surface modification approaches that can control the wettability of CNT carpets, and their applicability in water treatment applications.