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I have mine set up with a BIG skimmer, BIG refugium, Ozone (really helps) and lots and lots of macro algae in the display. I use RO water but found the macro was growing too slow for my liking, so have started adding a bit of tap water in with it. I now get much better macro growth and no bad algae really. I think macro and ozone are the key to less bad algae.
My FOWLR is set up the exact same as how I would set up a reef that needed pristine water quality for corals. I think if you take that approach, you will also have better success. I see a lot of people who don't care as much about water conditions because there are only fish and no corals. I think this is really bad because it leads to bad algae problems, disease and just because fish can handle nitrate at 40 ppm, doesnt mean they should. Sorry a bit off topic but water quality does effect algae growth more than anything else and it gets a little overlooked in FOWLRs in favor or a heavily stocked tank.
As someone else said, maybe you were overstocked???
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