A strong wind toppled your crane statue into the pond and his beak penetrated your rubber liner. Now what?
Empty the pond to below the hole. Clean the area around the penetration even if you have to scrub it (NO SOAP), rinse it and either wait until it is dry or use a hair dryer. Make sure you are plugged into a GFI outlet for safety's sake. When the area is clean and dry, you can use a tire patch to patch the hole. After all, the rubber liner is made by Firestone out of the same material inner tubes are made of. You can also buy patches or rolls of patching tape that makes it even easier.