Algae reactor. Is this right.

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A month ago I bought a Algae reactor to grow Chaeto and get on top of my Algae issues. I have to say it's doing a great job however the noise it makes from air bubbles escaping is driving me up the wall. From the pics, I have it in the 2nd chamber in 6" deep water. This is a red starfish reactor based around there skimmer as it has a dc controlled pump. Water gets sucked in the reactor and 2 open end tubes take the water back to the bottom, so in the reactor there is a 1-2cm air gap at the top. What I dont under stand is why the bottom chamber where the pump is doesnt fill fully with water. The air bubbles come out the back, increasing the pump speed just increase the rate the bubbles come out. Raising it doesnt make any difference either. I have put a sponge over the outlet to try and disperse the bubble noise but it doesnt make any difference. Any thoughts.

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