Nope, I don't think it will hurt. You are pulling water from roughly mid way depth wise in the pond, which will leave the lowest, warmest water undisturbed. I'm unsure whether you are planning on running the system all winter long.

Watch that you don't pump the "holding tank" dry before the gravity water flow catches up. I don't think that the 4" horizontal pipe, being gravity fed, will have enough flow volume to keep the pumps fed if the water column isn't sealed like a well casing with a submersible pump, creating negetative pressure to help the water along. But, that's just a WAG.

Interesting project! I'll be interested in how it turns out. Please take and post pics of how it's progressing.

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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).