The standard covers that come with Intex pools are a joke when wet, but dry they are fine. I always had this problem when it rains, as there would be a huge puddle on the top of the cover, about 8cm deep. I had to take the skimmer and manually scoop out the debris. I now have a new solar cover from Dolfino, which is much better. I used to just take off the cover when it rained, and attach the auto skimmer to get the debris before it settles to the bottom, and that worked for me. Is your filter the all in one unit that just hangs from the top rail?