If you have algae growing on the bottom pane of glass (besides coralline) in a BB setup you probably are not set up optimally for a BB system. For the best results in a BB system you need little rock (open scape) which best is suspended from the bottom some how or touches the bottom very little. No rock should touch any side pane and you need A LOT of flow to keep all the detritus suspended. An over sized skimmer should also be used. At this point you will probably still have some detritus and small particles build up on the bottom which need to be syphoned out every week or two so it is good to have lots of open space to get your hand it and clean.
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