Every couple of months I put my power heads and the pump for my skimmer in a 5 gal. bucket filled with 1 gal. vinegar and the rest water and run them for about 24hrs. They come out very clean.
I just try real hard to make sure the output is pointed down or to the side. It doesn't have a full five gallons though, just enough to make sure the pump doesn't suck air.
The lid is a good idea though, didn't think of that.
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