Repair a Rubber Liner

After we knew the water level was falling from more than pure evaporation, we bit the bullet and started to empty the pond. You will need something to put MOST of the water in, since it's "seasoned" and best for the fish if you can keep it. Be careful not to disturb the plants and fish any more than you have to. Watch where you step, and hope you can allow a spot for the fish to go and hide. The plants will be OK as long as the roots don't dry out.
This was the first hole we found when we removed the water. We used a standard rubber (EPDM) liner for the pond, but the root of a large reed punctured it anyway. As we continued to lower the water level, we found more holes, all in the same general area, The reed was planted as a marginal plant in the pond. It grew out of the pond along a fold in the liner, and turned around to find a way back in.
We found five holes in all - two on a flat shelf and three on the vertical side of the pond. We visited a local lawn and garden store and, on the advice of a friend in the pond construction field, bought two types of patching material. One rubber patch had adhesive on both sides, and can be used to seam two pieces of liner together to make a larger piece. The other only had adhesive on one side, but was larger so it covered the actual patch entirely, and then some.
We cleaned the area well with a stiff brush, then a bit with a brush with brass bristles, and finished up with abrasive cloth. The paper backing is removed from one side and the patch is burnished down after it's applied. Removed the top layer of backing paper and check the seal. With the holes on the flat shelf, it was easy to see if the patch actually did its job. Make sure you don't have any air bubbles under the patch. Now the second patch was prepared to go over this patch.
Remove the paper backing from the larger patch. Our advice is to use BOTH types of patches. This pond was over 10 years old, and this was the first time we had to repair a hole in it. I won't mind waiting another 10 if two patches will do it! Apply the patch, centering it over the bottom patch before pressing it into place. Make sure you have contact with the liner on all edges of the top patch.
Burnish the patches down well. This also can remove small air bubbles you may have missed, and also adheres both patches to the liner, AND together. After burnishing, let the patch warm up in the sun a bit, and then re-burnish and check for problems.
The holes on the vertical surface are a little trickier, and this was more difficult because we couldn't get rid of the fold in the area we were trying to patch. Prepare the surface of the rubber liner the same way so it's as clean as you can get it. Apply the double-sided adhesive patch, again working out the air bubbles and getting maximum surface contact.
We let the sun do a little more warming this time, and then checked contact and adhesion again before removing the backing paper. After we were satisfied with the first patch, it was time for the second layer. Again, make sure of proper contact.
Burnish the patches well, warm them and re-burnish, and then go have lunch. A little more sun-curing can't hurt a bit. If you're satisfied the holes have been adequately sealed, replace the water from your storage containers, re-float the plants, and feed the fish to make up for the stress you made them endure. That's it! The whole process was about two hours, start to finish, once the water was out.
P.S. - If you like, you can do a little thinning and other minor cleanup tasks while the water level is down, but don't let the plants dry out.