No toilet designed to use sea water should ever be connected to the fresh water plumbing and every toilet mfr specifically warns against it in their installation instructions. Reason: sea water can migrate into the fresh water plumbing, contaminating the fresh water supply...and so can bacteria from bowl. People do it and most have been lucky enough to avoid problems...but that's about like saying "I jaywalk all the time and have never been hit by a car or gotten a ticket for it"...sooner or later luck always runs out.
Toilets designed to use fresh water are all designed to use PRESSURIZED flush water...and instead of an intake pump have either a built in valve or a solenoid valve installed in the intake line that opens and closes much like a faucet does. The boat's water pump must be on to flush the toilet.
There's a very simple and inexpensive way to prevent odor caused by sea water left to sit and stagnate in the toilet intake:
Sink drain thru-hulls are below the waterline on almost all sailboats. So re-route the toilet intake hose to tee or wye it into the sink drain line as close to the seacock as possible because the connection must be below waterline to work.
This will allow you to flush normally with sea water. After you’ve closed the sink drain seacock in preparation to close up the boat (you do close all seacocks before leaving the boat to sit??), fill the sink with clean fresh water and flush the toilet. Because the seacock is closed, the toilet will draw the water out of the sink, rinsing the sea water out of the entire system—intake line, pump, channel in the rim of the bowl and the discharge line,(Water poured into the bowl only rinses out the toilet discharge line). If your toilet is electric, be careful not to let it run dry…doing so can burn out the intake impeller. Or you can keep the sink drain seacock closed except when it's needed to drain the sink and flush with fresh water down the sink all the time...your choice.
It may also be necessary to keep the sink plugged except when in use, with a rubber sink plug or by installing a conveniently located shut-off valve in the drain hose. Otherwise the toilet may pull air through the sink when you try to flush, preventing the pump from priming.
--Peggie