3 gpm = 4300 gallons per day. There is 27,000 gallons in one acre inch of water. That means it takes about 6 days to move it one inch. When you take into account fresh dry dirt and evaporation I'm surprised it's filling at all. I lost about a 1/4 a day from evaporation during the summer.
It has been unusually dry in your parts this year but don't worry, the rain will come at some point. And when it does I think you will hold fine. My only concern is that you didn't core trench the down side. If you did please disregard. If you didn't, once the pond is full and you get maximum psi at the bottom you need to check the backside for leaks.
