Sailmonkey ID'd the problem--dead and decaying micro- (and sometimes not so micro-) sea life in the toilet intake--line, pump
and channel in the rim of the bowl. However, it's unlikely that your toilet shares the same thru-hull as the sink drain (a simple and inexpensive mod as long as the toilet and sink are on the same side of the keel), and just pouring water
into the bowl and flushing
it won't solve the problem because bowl contents aren't recirculated through the intake...you wouldn't want them to!
So first, let's clean out the toilet intake. Remove the intake line from the thru-hull (close the seacock first!) and stick into a bucket of clean FRESH water to which you've added a quart of distilled white vinegar (available at any grocery store...may be in the cleaning
products section if not with the "cooking" vinegars) Flush the whole bucketful.
Now, as long as the intake line is off the thru-hull, this would be a good time to re-route it to tee into your head sink drain. Only part needed is a tee or wye (not y-valve, just a wye). The tee needs to be below waterline as close to the thru-hull as possible. 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). 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.
Questions? I'll be glad to answer 'em.