To utilize carbon nanotubes in real-world applications, we have to master their chemistry. At present there is a lack of understanding regarding what happens during basic manipulations, such as doping with acids, forming suspensions by sonication in water with surfactants, or detecting peroxides. We show that sonication of nanotubes in water leads to the in situ formation of molecular oxygen, causing doping, which can be quenched with ethanol. In the presence of the anionic surfactant sodium dodecyl sulfate, oxygen doping is overshadowed by doping due to the sulfate group. Stable suspensions of undoped nanotubes can be created with Triton-X spiked with ethanol. Hydrogen peroxide does not dope, but in high concentrations or in the presence of catalytic iron nanoparticles it decomposes to yield oxygen, which may dope. Hydrochloric acid does not dope, unlike sulfuric acid. Our results clarify the origins of doping while processing carbon nanotubes in water.