The Space Shuttle, the spacecraft in which I traveled myself, has engines that use oxygen and hydrogen. The only residue is water and that is not harmful.
However, the launch of the Shuttle is damaging to the environment: a great amount of exhaust gas is spread and up to today there is no other solution to make this less harmful.
Also, the waste that is left behind into space by astronauts can be a problem. In the past it was allowed to dump old satellites and waste of a space station into space, but nowadays that is forbidden.