Acids remove rust stains from canvas. Oxalic acid is sometimes used and is an ingredient found in some anti-rust products. Yet, it is a toxic substance, and requires careful handling. Instead of using a poisonous substance, like oxalic acid, another option is lemon juice, which is both acid and edible. How you go about removing the rust will partially depend on the canvas item. If it is a canvas cover, you can move it around in ways that you won't be able to move a canvas beach chair, where the canvas covering permanently attaches to the chair.
Cover the rust stain with table salt.
Pour lemon juice over the salt to make a paste.
Set the canvas in the sun, or soak the area in a pint of warm water.
Rinse off the canvas after the rust disappears.
Cement cleaner is sometimes used to remove rust from canvas. Removing the rust in this manner can possibly fade the area.