If the "smell in the air" is confined to the head, and is coming from the bowl with the first few flushes after boat has been sitting, yes...stagnant sea water and dead and decaying micro (and sometimes not so micro) animal and/or vegetable sea life left to sit in the intake line, pump and channel in the rim of the bowl is the culprit. That the odor
seems to be stronger and hanging around longer is a strong indication that you've pulled in weeds or a minnow that's taking more decompose. (Worst I ever encountered was the remains of a baby octopus).
Step 1. Buy a a couple of quarts of distilled white vinegar....and a bucket if you don't have one.
Step 2: Put one quart of the vinegar into a bucketful of clean FRESH water.
Step 3: Disconnect the toilet intake line from the thru-hull (might be a good idea to close the seacock first)...stick into the bucket of vinegar and water, flush the whole bucketful through the toilet.
That should clean out the system.
If you search the archives
, you'll find a lot of discussion about a way to prevent this problem by re-routing the head intake line to tee into the head sink drain line. That will allow you to flush with sea water normally, but rinse all the sea water out of the system before the boat will sit by closing the drain seacock and filling the sink with clean fresh water ...flush the toilet. Because the seacock is closed, the toilet will pull the water out of the sink, rinsing out the whole system...water poured into the bowl doesn't recirculate through the intake, it just goes out the discharge.