The aeration should help reduce the muck if it's stagnant and there isn't any O2 at the bottom. At only 3' deep, I don't know if that's true or not. There are shallow and deep water diffusers, and a very shallow diffuser that is like a soaker hose.

Lets see what an aeration expert has to say.

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3/4 to 1 1/4 ac pond LMB, SMB, PS, BG, RES, CC, YP, Bardello BG, (RBT & Blue Tilapia - seasonal).