In "Starship Mine," the baryon sweep is employed to purge the Enterprise of baryon particles. The sweep is deadly to common forms of organic life (and perhaps uncommon ones), so the ship is evacuated.
Is it stated anywhere how Captain Picard's fish were kept safe from the sweep? The captain has a fish in his ready room and some in his quarters.
Out-of-universe, I doubt the writers cared about the details of baryon-sweep planning to such a fine degree. However, I am interested to hear an in-universe answer, of course.