You'll probably never be able to manage your fish population well in a lake that large with the water / fish coming in from pond above so it may be more of a mitigation / improvement issue.

Would be interested in knowing pond depths and contour. Max depth? How much is shallow?

Would you be able to set up a siphon and drain out a large percentage of the water? That would possibly get a lot of those small fish out of the weeds and provide food for the big fish. After the muck dried out some, you could possibly take out some of the silt / etc. to deepen those areas and minimize weed growth to a smaller percentage of the lake.

I am fortunate enough that I have enough contour / height differences that I was able to install a siphon and pull water from my big pond (17 - 19 acres built in 2003). I used 8" heavy duty PVC (schedule 40 or 80?) and installed it with excavator. Put a small valve with riser at top so could fill pipe or open valve to allow air in and shut off in needed and another big valve near the bottom that we use to turn siphon on or off. I keep the top one closed. Works really, really well to adjust water levels.

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