The hull of my own boat is always well waxed and I really don’t get to much if any waterline staining. A good coat of wax, or a polymer sealer such as Awlcare, can go a long way to minimizing these brown stains. I did however leave my inflatable in the water for a few weeks and got enough staining to illustrate the process.
For Gelcoat, Not Painted Hulls:
This task is easy and is also safe for gelcoated hulls. While I have personally used mild acid formulations on LPU paints such as Awlgrip or Alexseal and Acrylic urethane products such as Awlcraft 2000 or Imron I don’t suggest it, nor do the paint manufacturers.
If you must use an acid on paint please be really, really, really, really careful and rinse it off immediately after the stain disappears DO NOT LET IT DRY. Do small 3-4′ sections before moving on and rinse, rinse rinse once the stain is gone. For a painted hull use the mildest acid you can find. I like a product called Spotless Stainless, which is citric acid based, not oxalic or hydrochloric based.
To clean waterline stains I use MaryKate On & Off Gel pictured here. This is a huge improvement over the regular non-gel On & Off or basic Oxalic crystals from the hardware store. It’s also a lot cheaper and stronger than products like Davis FSR stain remover, but works similarly.
There are a lot of products out there that contain an acid that will work but the On & Off Gel is one of my favorites. It also has much less “acid” odor than the regular On & Off and hits your nose a lot less forcefully…
This is also a great step to do before waxing a boat and it will whiten up most any old tannin/rust stained gelcoated hull.
Always wear rubber gloves & eye protection! Remember this stuff is acid. I use cheap chip brushes to apply it and toss them when I am done.