From what I know, there has been trace amounts (much, much less than 1% of the mass of the planet) of water (H₂O) observed in Jupiter. Both carbon and oxygen have also been observed in trace amounts, and if they come together in the form of CO₂, it would be a very, very small percentage of the total composition of the planet. The majority of Jupiter consists of helium and hydrogen gas.

Scientists determine the chemical elements in a planet from far away (such as with orbiting unmanned spacecraft) by recording the light that is emitted from the planet. Each element absorbs a small and unique portion of visible light, so if scientists see a dark spot in the spectrum of light they record from the planet, they know what element caused the dark spot, which tells them which elements are on the planet.