I have my main pump in a skimmer so there are two layers of filter pads over it to keep most the algae out, as well as a skimmer basket. The smaller pump at the bottom of the deeper end pumps up to a pressure filter and it also gets really clogged with algae if I don't keep on top of it. I have the algae under control now by cleaning and treatments including barley plus the weather has gone back to its usual cloudy and cooler so the growth has all but stopped except in the falls and tiny stream areas where I have string algae to stay on top of.
