I'm no expert but I suspect the smaller pipe is your primary drain; if the water gets high enough to get to the top, it drains through there. Then, I would guess the larger brick one is your secondary drain and that it is a little higher than your primary drain. As far as a leak, do you see any water around the edges of the pond where water may be escaping?
I think the only easy way to find the problem is keep observing, hoping to see where the water is going. Perhaps get out there on a raft and place some dye near the suspected leak points and see what it tells you. The water appears clear enough it may help.
The pipe in the middle that showed up (it looks like it is usually under water) probably has leaked along it, or is broken. I would suspect that first.
Agree with all the comments so far.
There must be clear signs of where the water is coming out of the pond.
It should drain down to the level of the leak which may enable an effective repair.
It may also be a good time to drain down the pond using a trash pump in order to do more extensive, long lasting repairs.
Actually the bricked up pipe was an old corrugated metal pipe it sits about 3 feet lower than the pipe in the center of the pond. I was told that capped pipe in the center of the pond was a emergency drain with a cap on it. I am guessing it is cast iron with a concrete base and a 45 bend thru the dike wall. It is slanted and loose, I have no idea if it was run thru the CMP metal pipe, I have never seen where it day lights out on the backside of the retaining wall. I will check it this weekend when I fly into NY.
Due to the volume of water in the pond, NY water conservation stated I can not work on it without P.E. stamped drawings if the pond is full. If I let it drain ( it is losing 2-3 feet a week ) I can fix it. I will just grout if full. From your experience how long will it take for the pond to refill. on average
Refilling of the pond is always a concern.
What is the water source? Spring, well, run-off?
A re-fill is completely unpredictable, though in NY, that will likely happen between January and April when evapotranspiration is lowest, and regular precipitation results in runoff. Unfortunately it usually means white stuff to make it happen.
This year was not the norm, with runoff events almost all summer that would fill a large pond overnight. If you are lucky, a single rain event can quickly top things off.
Note that if you plug and fill the existing drains, I would replace what you have with a siphon system since your pond is on the large side. As a backup, just rely on a grass-covered spillway on undisturbed soils.
The key is to be patient, and you can re-stock before the pond is full with FHM.
To add to l-squid's comments...
A substantial draw down in water levels for some durations of time does effect the fish population in positive ways (assuming the current pond is not vastly overcrowded).
