Remove the aquatic plants and fish from your leaking pond. As much of a problem as this seems to be now, your job will be exacerbated when the leak speeds up. Take the time now to remove your plants and fish and place them safely in an external tank or aquarium. A set of waterproof plastic storage containers can hold your fish and plants temporarily.
Observe your pond and the rate at which it is leaking. To track down the leak, you are going to have to allow your pond to drain through the leak until it levels off. Each day, use a yardstick to measure the depth of the pond and track the leak rate. This information will be useful later.
Look for the puncture or hole. Once the pond levels off and stops leaking, you know the hole in the liner is somewhere just above the current water line. Begin examining the liner. Get down on your hands and knees and carefully use a sponge to wipe the liner clean. This will help you locate the hole or holes. Finding one hole does not mean you have found all the holes. Continue around the water line until you have checked the entire exposed liner. Make a circle around the puncture marks using your grease pencil.
Pump another 4 to 5 inches of water out of the pond. You want to make sure the water line is well below the punctures you have identified in the liner, so that a breeze or rainfall won't move water onto or above the patches before they have had a chance to set.
Patch your punctures or holes, reading and following the instructions on the patch kit. You will have to thoroughly clean the area around the puncture or punctures, and most patch material requires 24 hours to dry.
Refill your pond. Once the patches have had a chance to cure, add water to your pond to its normal level. Hold off on replacing your fish or aquatic plants, however. You want to ensure that you have in fact patched all the leaks.
Observe your pond for a few days. Is the water level falling? You should have a pretty good idea of the rate of the leak per day from the measurements you took earlier. If the pond seems to be leaking at a somewhat slower rate, you might have another leak higher in the liner than your patches. Repeat the steps above to locate and repair any remaining leaks.