Modern boat canvas is usually made from a synthetic fabric, like Dacron or nylon, rather than cotton. Since your boat's canvas is regularly subjected to a wet--or at least damp--environment, mold prevention is the goal of canvas maintenance. Elbow grease, without harsh chemicals that damage the canvas, can prevent mold from gaining a foothold and is no more than an afternoon's work.
Items you will need
Woolite
White vinegar
Clear water
Soft bristle scrub brush
Remove the canvas from the boat and spread the canvas over a smooth surface. If you try to scrub the canvas on a gravel or paved surface, you may damage one side while scrubbing the other.
Mix 2 tablespoons of Woolite and 2 cups of white vinegar in a gallon of water. Do not use liquid bleach on boat canvas, regardless of the type of material. The active ingredient in liquid bleach is sodium hypochlorite, which will strip the protective coating from the threads that are used in the canvas.
Rinse the canvas with clear water. Scrub the canvas with a soft-bristle deck brush and a mild liquid dish soap to remove loose dirt, salt and sand.
Use a brush with soft bristles to scrub the parts of the canvas that show any evidence of mold with the Woolite/vinegar/water mixture. Continue to scrub these areas until the mold has been physically removed.
Hang the canvas so that both sides are exposed to the air and allow it to air dry undisturbed. When the canvas is completely dry, fold it or roll it and store it in a clean, dry place.