Stains on vinyl liner

I have a built in pool with fiberglass sides and a low hung vinyl liner. The last 3 years opening the pool, I have problem with what I think are organic stains from worms in the pool over the winter. The water is clear but the stains on the bottom which are all over the liner especially in the deep end by they drain. Over the course of the summer the stains gradually go away either from the sun or chlorine bleaching them. Usually by closing time these stains are mostly gone only to begin again when opening. My question is does anybody out there know how to get rid of this stains immediately or anything I could put in the water to prevent this happening over the winter.?

thanks hal