i can attest to the "water through the cover" theory. i used to panic about how much my water level went down over the winter (inground pool, solid cover). i would leave the water level up at closing (late september), and it would be down a foot and a half at opening (late may). i kept thinking that there just HAD to be a leak, but i wasn't losing water during the summer. since i pump water off the cover several times a winter, someone finally pointed out that i was probably pumping out pool water since there was some "pass through equilibrium" going on.
sure enough, my old cover was starting to get ratty so i put a brand new one on last fall, and i still had water loss, but not nearly as much.
if you take a look at how those covers are really made, it's not all that surprising. they're basically woven from strips of plastic, and the weave allows water to pass through very, very slowly.
not to worry... you could EASILY have lost 3" from pass-through.

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What I've noticed on the many pools I've worked on is that a hole in the cover is the prime suspect, if you have one and try to pump the water off your cover, you will lose pool water (however, the faster you pump off the cover, the less pool water you'll lose). I can't question that some water may make it through a 'holeless' cover, but I think the amount would need to be measured with a well calibrated micrometer.

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