Hello Jason, While we try and design and build our ponds to never leak by doing proper soil testing before we start digging with the shovels the reality is that certain conditions can cause a pond to leak. We don't specialize in repairing a leaking pond as that often involves fixing someone else's shoddy pond building or poor choice for a pond site. That being said, whenever we work with a contractor to seal a pond we almost always use Soilfloc pond sealer.
Soilfloc® shoud be applied when the ditch, pond, or canal has water in it & is currently leaking as the leak in the dam or basin creates a natural suction that will draw the Solifloc polymers into the problem areas & seal the leak or leaks.
If you know where the leak is can concentrate the application in that area, but it is strongly recommended that the rest pond, canal or basin be treated as well to provide a consistant seal. This also helps if soil consistancy could lead to future leaks. Application is best done when the pondwater level is at least above the problem area and to the full basin volume of possible. Read more about Soilfloc Pond Sealer
Another product used is bentonite. Bentonite is amazing stuff and it is actually the same stuff that is in clumping kitty litter! I should know because I have friends who use raw bentonite mixed with sand as an inexpensive cat litter! Bentonite, or sodium bentonite clay as it is also known, swells up to eighteen times its dry size when it becomes wet. Expanded bentonite forms an impermeable gel seal which makes an excellent pond sealant. Bentonite is environmentally safe and does not affect the water, livestock, or wildlife. When properly applied, it will not harm fish. For these qualities, bentonite also makes an excellent liner for new pond construction. When sealing a leaking pond to prevent water loss through seepage, sodium bentonite can be applied directly to the soil in the pond bottom or it can be sprinkled on the surface of the water and allowed to settle to the bottom. There are three basic methods: the blanket method, the mixed blanket method and the sprinkle method. Sodium bentonite is easily applied. In the case of small ponds, it can be applied with simple hand tools and for larger ponds, with ordinary farm equipment. J. P. Self and Associates only sells granular bentonite by the tractor trailer load, 45,000 lbs. minimum,unless local pick-up.
I've heard of using Sodium Bentonite or a product called ESS-13. Check out http://www.pondsealer.net/ for the bentonite and Seepage Control http://www.seepagecontrol.com/ for the ESS-13 product. Depending on the size of the pond a liner may be the best option but you can try the three sites I suggested.
Soilfloc pond sealant is available here