Fate and transport of carbon nanomaterials can be strongly dependent on the interaction with secondary particulates in the aquatic systems. Bio-particulates in water, e.g., viruses with charged and hydrophobic surface moieties, may profoundly influence the interfacial behavior and hence the environmental fate of nanomaterials (and vice versa). This study systematically evaluates the interfacial interaction of acid-functionalized multiwalled carbon nanotubes (MWNTs) with MS2 bacteriophages, or heteroaggregation behavior of these particulates, under mono- and di-valent cations and with Suwannee River humic acid (SRHA). Results indicate that the highest concentration of MS2 (i.e., MWNT:MS2 of 100:1) renders exceptional stability of MWNTs, even in high salinity conditions. However, at lower MS2 concentrations (i.e., MWNT:MS2 of 1000:1 and 10,000:1), the suppression of MWNT heteroaggregation rate is not as significant. The observed enhanced stability is likely caused by the preferential attachment of the MS2 capsids onto MWNT surfaces, which is mediated by electrostatic attraction (between negatively charged oxygen-containing moieties on MWNTs and positively charged amino acid residues on MS2 surfaces) and/or by MS2 capsids with positive hydropathy index (indicating strong hydrophobicity). Presence of SRHA also shows stability enhancement; however, at lower MS2 concentrations, SRHA dominated the heteroaggregation behavior. These results implicate that preferential interaction between virus capsids (i.e., MS2 and may be other waterborne viruses) and carbonaceous nanomaterials may influence environmental transport of both in aquatic environments.