All depends on the waterway and the nature of the job.
First consideration is whether or not the waterway is federally controlled or state controlled. Any coastal waterway, waterway used for commercial traffic (Missouri, Ten-Tom, Mississippi, Hudson, American, Columbia river systems are but a few) or any waterway that is a state line (Great Lakes, Lake Tahoe, Lake Texoma, Lake Champlain, etc.) are all federally controlled waterways- so you would need to be licensed if being employed to carry fare paying passengers. If one is hired as a captain on a private vessel to act as skipper in command for non-paying passengers, then the captain's license requirement is not applicable.
State waterways come under the jurisdiction of the particular state- for example, only a Texas state license is needed to be a charter captain on Lake Travis.