Welcome to PBF Rebuck!
I'm not a pro but here's a couple of thoughts...
IMHO All ponds lose water to some extent, even if just thru evaporation. As Esshup pointed out, if you have a "leak" that can increase those loses significantly.
Perhaps another consideration...You stated that your water flow in is only 3 GPM. You haven't provided any info on size of the pond but, unless the slope is straight up and down, the amount the pond rises per unit of water input will decrease as the pond gets deeper and the surface area increases. It may be you are reaching equilibrium where losses are near 3 GPM so the pond will continue to rise very little, if at all. Do you have a substantial area of water shed that can provide a large influx of water during a significant rain event to help fill the pond?
Good luck and, again, welcome to PBF!
Bill D.
Last edited by Bill D.; 10/24/16 08:00 PM. Reason: Typo