Many drugs deteriorate over a given amount of time, the substances they deteriorate into with aquatic medications are harmless to fish, if not they would be useless for medicating fish. This is very similar to the half-life of drugs taken orally by humans or other mammals. As with the half-life of drugs, this rate of deterioration depends on the specific drug. Some drugs, such as Gentamycin, deteriorate very slowly, and require one dose, with no water changes at all. Others, such as Metronidazole, deteriorate quickly, and can be redosed every 8 hours.
Maracyn, which is Erythromycin, is a good medication for most gram-positive diseases, fin rot, popeye and such. Maracyn II, which contains Minocycline, a synthetic form of Tetracycline, targets gram-negative bacteria, septicemia, dropsy & such.
There two products are the most readily available antibiotics to people in the US, any decent shop carries them. They are the best starting point with most bacterial diseases, which for a definite identification would require dissection, and staining slides. This obviously is not an option for the hobbyist, but is what large hatcheries do when there is a problem. Seeing as we usually don’t want to sacrifice the fish here it is a sort of shotgun approach, but one that is effective, and with the longer term treatment nearly eliminates the chance of creating a drug resistant strain.