While earlier studies have identified the antibacterial activity of carbon nanotubes (CNTs) and proposed that cell membrane damage by direct contact with CNTs is likely the main toxicity mechanism, the relative importance of chemical versus physical properties of CNTs in controlling their bacterial cytotoxicity is understudied. Given that CNT is commonly modified via acid treatment to enhance its dispersivity and surface chemistry, in this study commercially available multi-walled carbon nanotubes (MWCNTs) with high purity were processed carefully by acid reflux, resulting in differences in surface charge of MWCNTs without altering their physical properties. The surface condition of MWCNTs was also modified by adsorption of organic matter to compare bacterial toxicity of functionalized and non-functionalized MWCNTs in suspensions. Results show that although overall electrostatic repulsion and steric obstruction resulted from surface modifications led to elevated dispersivity of MWCNTs and mitigated toxicity on planktonic Escherichia coli cultures, no correlation between the dispersivity and bacterial toxicity of MWCNTs was observed, suggesting that dispersity alone may not be a proper index to estimate the CNT antibacterial effect on planktonic cells in the aqueous phase. In addition, viability recovery of MWCNT-treated cells was observed to be nutrition level-dependent, implying that availability of proper nutrients may be another important factor to be considered when assessing the ecotoxicity of CNTs in the aquatic system.