Air in pool equipment?

My pump, filter, and equipment is all about a foot higher than the pool itself. No matter what I do, air always seems to get into the system. There is still plenty of water in the pump, but always a few inches of air at the top. It's only totally full when it has rained. There are no leaks as I've had every joint checked. I can let the air out at the filter, but it always comes back. Is this just because the pump is higher than the pool itself? Anyone have any experience with this kind of thing.