A nuclear thermal rocket works just fine in atmosphere. It has a similar profile to chemical rockets, in that you can tune the reaction or the bell nozzle to work well in atmosphere or in vacuum. The biggest problem with using this as a first stage is dealing with the legal and social logistics of running a nuclear reactor that isn't yet on an escape trajectory.
A solid core NTR exhaust might even be rather clean. Liquid or gas core NTR, not so much.
And if someone is planning to launch a nuclear salt water rocket inside the atmosphere of an inhabited planet, you certainly have bigger issues to worry about.
