When allowed to sit and stagnate, even humidity and rain water can turn into a "primordial soup" that can smell like a swamp or even a sewer. So the source of that water is far more likely to be a leak on deck--possibly the companionway hatch or frame, or rail stanchion(s) in need of re-bedding--that's been running down and collecting there for some time than it is from the toilet or sanitation plumbing. In fact, the leak could be just about anywhere on deck 'cuz it's not uncommon for water to migrate to a lower place in the boat instead of collecting directly below its "point of intrusion." I wouldn't rule out a pinhole leak in your fresh water piping either. Whatever the source it needs to be found and fixed 'cuz left alone it can result in rot.