Carbon nanotubes (CNTs) with various diameters and defect densities were added to a microbial reactor containing Cupriavidus necator, and the effects on bacterial growth and biosynthetic activity to produce poly(hydroxyalkanoate)s were investigated. Although growth was not affected by any of the CNTs, polymer biosynthesis was depressed by thinner and defect-rich CNTs. The Raman D-band was found to be insufficient for characterizing the CNTs for microbial toxicity.