Quite often diatoms will give way to cyno bacteria (purple sliime) which will in turn give way to hair algae. 3 months is within reason for the diatoms to still be going strong. How long ago did they start? Also, what is your substrate? Not playground or local sand I hope.
A couple of tips that may help are; get as much flow near the sand as possible without kicking it all over the place and resist the urge to re-auqascape or move rocks around.
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