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nikon is right...time.
Also, diatoms are an indicator of high Nitrates and/or Phosphates. What are you using for source water? Reverse osmosis/deionized water is your best, though fairly expensive to purchase a RO/DI unit, it will save you money and headaches in the long run.
Besides water quality, protein skimming and kalkwasser dripping will help your water quality and combat the diatoms. They will go away eventually.
Good circulation is also important so that there are no dead spots in the tank. You can blow some of them off the rocks with a turkey baster.
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Hindsight is 20/20.
Current Tank Info: 300 gal, 125 gal, 125 sump
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