I'll wager that it's not algae, but some other kind sediment you're seeing.
I think if it was algae the water wouldn't be clear. The algae would still be alive and not dead on the bottom.

If you use a mesh cover (as I do too) expect all manner of stuff to blow in, like tree pollen, etc.
But how does your water stay clear when you use basically the same technique as I do, and mine is (was) pea soup.


Chuck