I would guess your loss in water over the summer is due to evaporation. My little pond holds 1 acre foot and lost about 16" last year strictly to evaporation. This year will probably see the addition of a water line from my well to help keep it more full.

I am strictly watershed filled, with a large portion coming off of my neighbors lot. It never fails that I get a bloom after every significant rain event, even using dye in the pond. His septic discharges to the opposite side of his property and he never uses fertilizer, but the nutrients from cut grass and the treeline between us is enough.

With the creek running through other properties, those plots fertilizing and possibly discharging grey water from their septic systems into the creek, you definitely have a greater potential for high P and N being pumped into the pond.

Is the creek full of algae or is it clear most of the time? That might be a good indicator. My pond overflows into the drainage ditch and it sometimes gets loaded with algae after a big rain too. My side of the road will have algae, the other side, none.

I'm no expert, by any means, this is all pure speculation. Just some food for thought. Hope it helps.
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.10 surface acre pond, 10.5 foot deep. SW LA. The epitome of a mutt pond. BG, LMB, GSF, RES, BH, Warmouth, Longear Sunfish, Gambusia,Mud Minnows, Crappie, and now shiners!!...I subscribe!!