Rocky Lou,
As a veteran of calamitous stink in the San Francisco Estuary, let me chime in to help out.
First, as you have probably noticed, the smell on the first flush can be gruesome. This, as noted by an earlier comment, comes from the fact that the estuary is highly productive, with lots of nutrients and critters (mostly phytoplankton and zooplankton in your case). The water from the last raw water flush you did before you buttoned up your boat stays in the lines. Aerobic decay uses up all the oxygen trying to break down all the organic stuff in those raw water lines. Then anaerobic decay sets in and you get a stinky mess when the oxygen gets used up.
So when you come back to your boat and make the first flush, all that nasty, foul-smelling organic mess goes right into your toilet before going into the holding tank. The stink can be overwhelming. Indeed, if you have someone you want to embarrass—at least in the SF Estuary—have them be the first to flush the toilet after a couple of weeks. They and all your guests will be gassed out, with most of the smell coming from the toilet, not the vent line. It is quite the conversation starter and all the abuse will be directed at the one who flushed the toilet. Add all the enzymes you want to add to the holding tank will not prevent the first flush stank. As one person noted, you can chlorinate things by adding some to the raw water strainer. I never have.
The best way around this is to go with a fresh water flush. This not only does not smell in the head, but it reduces the organic load to your black water tank. You will read some pretty elaborate freshwater flush plumbing descriptions on this site. But the simplest thing to do is just pull out the faucet on the sink, turn it on full blast spray, and push the “drain only” button sequence (hold down both buttons on our 29CB). This full blast also allows you to clean the toilet if it needs it.
Which means you have to tell your guests to let you flush the toilet for them. Awkward but necessary.
Two final things. First, if you are going to be out on the water for awhile and want to conserve fresh water, you are going to have to flush using raw water a couple of times to get rid of the smell. Once the smell goes away, just use raw water flush and you are good to go. Second, this advice does not apply everywhere. We moved our boat to Elliot Bay Seattle from Pier 39 in San Francisco. We have only occasionally had a first flush calamity and exquisite social faux pas since productivity of the waters in the PNW is so low compared to San Francisco (which is why the water is so clear). So it matters where you are. In the Delta, despite the green water with harmful algae in it, you should be fine.
Boats are just a bunch of elaborate work arounds with even more elaborate rationalizations to justify them.
Jeff
