This work was designed to improve bacterial biodegradation of coomassie brilliant blue and methylene blue dyes by applying carbon nanotubes to facilitate bacterial cell feeding for dyes biodegradation. A bacterial consortium and azobacter were investigated, and conditions for improved biodegradation were optimized. The methodology included; first stage activation of carbon nanotubes by pretreatment with nitric acid for 6 h, washing, and drying at 105°C. The second stage included optimization of biodegradation conditions, using 20 ml glass tubes containing 12 ml of nutrient broth media inoculated with 1 ml of the bacterial source samples. Coomassie brilliant blue or methylene blue (10 mg L−1) was added to the mixture, and the decolorization efficiency was evaluated over time. For the primary adaptation of the biodegradation process, the removal efficiencies for coomassie brilliant blue were 70.2% and 69.2% when using a sand consortium and azobacter, respectively, and for methylene blue they were 81.0% and 82.6% with a sand consortium and azobacter, respectively. The biodegradation process exhibited maximum efficiency at a temperature of 30°C with shaking at 150 rpm. After applying the carbon nanotubes, the removal efficiencies were improved and those for coomassie brilliant blue were 95% and 93% for the sand consortium and azobacter, respectively, and 96% and 99% for methylene blue with the sand consortium and azobacter, respectively.