Most marine canvas covers are made of Sunbrella or other like material, which are woven acrylic fabrics that are water repellent, mildew resistant, and UV resistant. Salt water leaves behind a residue that holds moisture on the surface, which will result in mildew; if you wash with a solution of non-detergent soap and warm water it greatly reduces the chance of mildew. Avoid detergent-based soaps, as the detergent will damage the finish and make the canvas vulnerable to the elements. Sudbury, Lux and Ivory Soap are good soaps to use, as are liquid dishwashing soaps. Do not allow the soap to dry: Immediately after washing, rinse the canvas thoroughly with cool water to remove all soap residues. Do not fold or store the canvas while it's wet.
You can apply a water-repellant coating to the canvas to help keep it in good condition, but make sure the water-repellant is compatible with your canvas material! I have never had to use water-repellant on any of my canvas. Conventional cotton canvas typically doesn't need waterproofing; its waterproofing characteristics arise from the way the cotton fibers swell when they get wet. The swollen fibers seal the canvas weave; so classic cotton canvas does fine without any special waterproofing. But cotton canvas isn't used on recreational boats much anymore, but I don’t know how old your canvas is. Cotton does tend to mildew and can be damaged easily by bird droppings and similar debris. Most marine canvas today is made of a woven acrylic or vinyl-coated polyester. This is breathable, which helps it resist mildew better, and it holds up better under damaging UV rays. It also has better resistance to stains. But acrylic canvas needs a special chemical treatment to give it the needed water repellency, and the chemical treatment can lose effectiveness over time, particularly if the canvas is cleaned with detergents, or scrubbed vigorously. Acrylic canvas used on boats is likely to start losing its waterproof characteristics after a few years — the owner's maintenance of the canvas and where the boat is kept and stored can make a big difference in how long the initial waterproofing lasts. Acrylic canvas such as Sunbrella can be re-waterproofed, but it is important to use the right type of formula. Never use a silicone-based agent on acrylic canvas. The factory waterproofing uses a fluorocarbon, which is incompatible with silicone and that will result in a patchy and ineffective waterproofing. Fluoropolymer and petroleum waterproofing agents are the best agents to use to re-waterproof your canvas. These agents are compatible with the original treatment, and they provide excellent, long-lasting results.
All marine canvas resists mold, mildew, and U.V. light. If you cover the canvas with a tarp you should be fine and the tarp will add some additional protection for your canvas. It will not increase any chance of rot! Help prevent the growth of mildew on your canvas by spraying with a solution of 50% white vinegar and 50% water. Keep it in a spray bottle, and spray it on your canvas covers whenever you wash down the boat.
Use a clear silicone spray to lubricate the zippers. If you don’t you may be replacing a zipper. Spray the silicone onto the zipper and work it back and forth into the zipper. Use the same spray to lubricate snaps or other fasteners in the canvas. Avoid using petroleum products, such as Vaseline and avoid getting the silicone on your canvas.
I used to leave my canvas on and just cover with a tarp for the added protection. I would tie it down as tight and close it up as best I could. I would recommend the use of an Air Dryer Dehumidifier in the cabin to reduce mildew. And if you have an engine compartment… leave a light bulb on to reduce the moisture and prevent corrosion.
Wow... this ended up being more than my 2 cents!
But, I have been dealing with canvas for over 35 years.
Charlie