When we put in our 1.5 acre pond about 5 years ago, after a promising initial start (I posted on here that it was "holding like a jug"), it kept developing sink holes in a deep, rocky area in the bottom of our pond. In my case it was a self inflicted wound & lesson learned the hard way - don't ever blast rock for additional depth and think you can later seal it. Hard to believe, but it seemed like a good idea at the time!
It's a long story, but after about 3 years trying a number of approaches to plug the various holes and cracks in the rock, including clay and bentonite, and having the material always give way underneath due to the water pressure, creating new sinkholes, we were literally out of options. Lining the entire pond was not feasible from a budget perspective, especially because the entire bank of the pond was lined in probably 1000+ yards of rock rip-rap (I'll bet you can guess where that came from - yep, the hole we blasted).
As a last resort we tried a synthetic liner on the bottom of the pond in the area with the sink holes.
I'm not recommending this approach at all, but what we did was have our contractor dig a trench all around the area on the bottom of the pond with the leaks, installed the synthetic liner and cut the edges of the liner so that they were at the bottom of the trench and then back filled the trench with clay, essentially creating a pond in the bottom of our pond. The risk was and is that the water will work its way under the partial liner and cause it to float out and let the water out the bottom of our pond again.
So far the patch has worked (knock on wood). The pond has now held for two years with no signs of any further sinkholes or problems with water infiltrating behind the liner, just some seepage in another area that we're working on next.
Again, I am not advocating a partial, underwater liner as a good way to go. We just had no other choice for our particular situation. I don't know if it would work in other circumstances (and we certainly weren't able to get a warranty from the contractor or the manufacturer that it would definitely work for us). It was just an unorthodox solution that seems to have worked for us.
If it were me, I would do what the other posters suggested and try packed clay. Also, if the fissures are visible, before putting the clay down you might want to try and work some crushed gravel or landscape fabric into them to clog them up and provide support for the clay liner.
From first hand experience, a leaking pond can almost drive you crazy. Good luck!
