A good trick is to actually run the powerhead in the vinegar solution for a 24 hour period (make sure the water level isn't so low you blast water everywhere!). This REALLY gets the whole thing clean and makes the toothbrush cleaning at the end that much easier. I do this monthly to all my powerheads and that seems to keep them in good working order.
Fill a 5 gallon bucket 1/3 up with water, giver er' a few heavy pours of vinegar, toss the powerheads in and turn them on. A few hours later they will be just as clean as when you got them. Feel free to toss your skimmer in there with them....works for those too.
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