Recommend you take several soil sample from the watershed and send to TAMU for testing.
The 3 ton of ag lime you applied sounds way light to me. Generally you'll want to add lime at the same rate called for in your soil sample.
In my part of the world that amounts to 4 ton/acre repeated every few years to maintain pH around 6.
If it's possible for you to purchase and apply limestone cobble in the 4"-12" size range in a few place around the waterline
that will be long-term help. Doing the same in the stream bed that feeds your pond would also provide benefit long-term.
Stressless made a good point of differentiating between alkalinity and pH, and provided a couple links to reference material.
