How do I get rid of the wrinkles when filling the AGP?

I am frustrated with trying to get rid of the wrinkles on the pool bottom. I've been on my hands and knees with an inch of water on the bottom and cannot get rid of them. I've used the pool brush. I'm going to try a plunger next.

Is there an acceptable limit to wrinkles? Will some of them go away once the pool fills up? They are not big wrinkles. Definitely not sharp creases.