This study evaluates the cytotoxicity of four carbon-based nanomaterials (CBNs)--single-walled carbon nanotubes (SWNTs), multiwalled carbon nanotubes (MWNTs), aqueous phase C60 nanoparticles (aq-nC60), and colloidal graphite--in gram negative and gram positive bacteria. The potential impacts of CBNs on microorganisms in natural and engineered aquatic systems are also evaluated. SWNTs inactivate the highest percentage of cells in monocultures of Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus epidermis, as well as in the diverse microbial communities of river water and wastewater effluent. Bacterial cytotoxicity displays time dependence, with longer exposure times accentuating toxicity in monocultures with initial tolerance for SWNTs. In Bacillus subtilis, an additional 3.5 h of incubation produced a five fold increase in toxicity. Elevated concentration of NOM reduces the attachment of bacteria on SWNT aggregates by 50%, but does not mitigate toxicity toward attached cells. CBN toxicity in bacterial monocultures was a poor predictor of microbial inactivation in chemically and biologically complex environmental samples.