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I've always heard that BBA tends to break out when Co2 levels become inconsistent, or drop - as has happened in my 55 gallon. So, I'm taking the Tom Barr method: Increase Co2 and decrease light. Trouble is, I'm not sure if my increasing Co2 is working that well! I also beat BBA with an excess of Flourish Excel in my 29 early in that tank's lifetime, but I don't like to go that route with my 55. Anyway, that's my suggestion: Increase Co2 and decrease light. I would guess the clogged reactor had more to do with it than you think.
 

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I've never had Blue Green Algae (knock on wood), but I did beat Black Beard Algae in my 29 with Flourish Excel. I saw it dying. It was quite fun to watch it die. My plants on the other hand, were quite happy. (no fish in the tank at the time as I killed the CAE in that tank with an OD of Flourish excel as well, entirely accidentally). After that, I added straight ammonia to the tank as well - no problems. No more algae. VERY high light as well.


My 55 is not as easy.
 
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