Here in southern Florida I would first wash with a detergent using a bristle brush and rinse well. Then I would mix 1/2 cup household bleach & 1/2 cup of the soapy water from the wash. Take a Q tip and dab the mildew spots (could also use a tooth brush) until they disapear. Try not to get any of this stuff on the seams as the bleach is not good for the threads. Rinse really well. That should do it.The clorene is what kills the mildew.<br /><br />I have had mildew really bad and had to scrub with Comet and rinsed really well. I would avoid if possible but it does work. Also it is very important to keep the canvas up so that it is exposed to the sun.
Jack Shellac and Solittle:<br /><br />Thanks for the response. Guess I'll break out the bleach. Unfortunately, it's not just a few spots; it's spotted ALL over (like dots about the size of a nickel). Should I treat it with some sort of water repellant after? Thanks for the responses. Much appreciated.
When they are "really bad" you may want to take it completely off of the boat and off of the frame. Lay it out in the driveway and scrub away. I have never had a really bad one come back perfect but close. Use the Comet, stiff brush and rinse 3 times as long as you think it needs. I have never had the fabric of a top go but seams seem to last 4-7 years. <br /><br />I doubt that any water repelant will help but it sure can't hurt. I tried some of that stuff sold in gallon cans by an Army/Navy store. The product was marketed for tents. It accomplished nothing. You may have a better experience.
I got obsessed with trying to clean/prevent mildew on my cover; ended up spending more time on the mildew than I spent boating. <br /><br />I learned that aggressive cleaning can destroy waterproofing and weaken seams and fabric, never did figure out how to keep the cover looking new...learned to live with the mildew.
"Scrub Free" Stain and Mildew Remover works great! Just spray it on, let sit for a couple of minutes and hose it off. Mildew and stains are gone. Been using it for years with no side affects! Can be bought at Walmart and other discount stores! Must say "Stain and Mildew Remover", as they make other similar products, so look at the bottle closely.