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This is a real problem in my area...SW Florida...if you have a white hull & no bottom paint the water stains it a brown color.
There are products that can be used to remove this...if you can get to all the areas of the hull affected. I believe these products are pretty rough on fiberglass and can etch or pit it over time?
Wax may help for awhile but hard to do often enough. Any thoughts? If I get a new boat built, I may have it a solid (non white) colored hull partly because of this.
Have you tried FSR (Fiberglass Stain Remover) it is avilable at most marine stores. It does a great job on rust stains etc., and does not harm the gelcoat or the finish on it. Give it a try.
This stuff is a strong hydrochloric acid solution which requires careful use--good ventilation, gloves, eye protection too. On the plus side, it's very easy to use. Wipe some on with a sponge (and gloved hand), then rinse it off after drinking approx. 1 beer. Your boat will be gleaming white again. I bought this product at Boater's World. West Marine and others probably also carry it.
Oxcalic Acid, or one of the deck cleaners you can bye in any paint store for removing tannin stains or wood deck cleaning. Oxcalic Acid is cheap and works great.
You could have a stain that is the result of a chemical reaction to sunlight. There are numerous way that this could happen. If all of the above methods fail to remove the stain, and, if it bothers you enough, you should consider taking the boat to a fiberglass repair facility and have the stain buffed and regelcoated. I know of all the products listed above; however, they might prove to be insufficient.
I'd be careful using the acid based cleaners, especially while the boat is on a trailer or lift. I made that mistake with my last boat. The acid based cleaners definitely removed the stain, but even after thorough rinsing, I was buying a new trailer soon thereafter. IMHO, the only way to avoid these stains is to get the boat out of the water as soon as you're done enjoying it. That can be a pain sometimes, especially when it's more convenient to leave it at the dock to enjoy after fishing festivities. It's a simple matter of how much time the boat spends in the water with an unpainted bottom.
Since its an acid stain why not try a product that has alkali to balance the PH...and since its not an acid it won't eat metal like a strong acid would.
I used to use Starbrite hull cleaner. Again, this is an oxalic acid, but already in a concentrated liquid. I applied mine with an old foam mop to keep it off the trailer. Let it sit, then rinse thoroughly (including the trailer).
"Tannin" stains on white hulls? 
