Peggy Hall has a book about such things. Here is a post from a while back.. This lady knows her stuff:
If you're only cleaning the tank, not the plumbing too...
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you're only doing half the job. Although most people think only in terms of the tank, the plumbing is actually the source of most foul water, because the molds, mildew, fungi and bacteria which cause it thrive in damp dark places, not under water. Many people—and even some boat manufacturers—believe that keeping the tanks empty reduce the problem, but an empty water tank only provides another damp dark home for those “critters.” To do it right, use a solution of 1 quart bleach/50 gal water....fill the tank, then turn on every faucet on the boat. When the water coming out smells strongly of bleach, turn off all the faucets, but leave the pump on to keep the system pressurized so the solution stays in the lines. Leave it in the system for at least 3 hours, but no longer than 24 hours. Then drain the tank through every faucet on the boat. Fill the tank again with clean water...drain again through every faucet. To remove excess chlorine taste or odor which might remain, prepare a solution of one quart white vinegar/five gallons water and allow this solution to agitate in tank for several days. Drain through every faucet, then flush the system with clean fresh water. This will also get rid of any anti-freeze taste/smell. People have expressed concern about using this method to recommission aluminum tanks. While bleach (chlorine) IS corrosive, it’s effects are are cumulative. So the effect of an annual or semi-annual "shock treatment" is negligible compared to the cumulative effect of holding chlorinated city water in the tank for years. Nevertheless, it's a good idea to mix the total amount of bleach in a few gallons of water before putting it into a metal tank. Be sure to turn off the water heater at the breaker before beginning the recommissioning...do not turn it on again until recommissioning is complete. An annual or semi-annual recommissioning according to the above directions is all that should be necessary to keep your water tasting and smelling as good as anything that comes out of any faucet on land. If you need to improve on that, install a water filter. Just remember that a filter is not a substitute for cleaning out the system, and that filters require regular inspection and cleaning or replacement. To keep the water system cleaner longer, use your fresh water...keep water flowing through system. The molds, fungi, and bacteria only start to grow in hoses that aren't being used. Before filling the tank each time, always let the dock water run for at least 15 minutes first...the same critters that like the lines on your boat LOVE the dock supply line and your hose that sit in the warm sun, and you certainly don't want to transfer water that's been sitting in the dock supply line to your boat's system. So let the water run long enough to flush out all the water that's been standing in them so that what goes into your boat is coming straight from the water main.
