I seriously doubt that deepening your pond would affect your well. There's always the risk that deepening it might cause it to leak, especially if you deepen the parts you can reach to stratigraphically below what is now the deepest part. And I suppose, if it leaks, it could leak into your well. And then there would be the question of whether it could contaminate your well. Any water that reached your well would be filtered through at least 25 yards of something. I remember another thread that I think said there is a requirement in one State that the water well had to be at least 5 yd from the nearest pond.
I'd be a little more concerned about the movement of heavy equipment near the well. Depending on how the well is constructed, shaking might harm it.
