I have a liner that is rubber, it's a fairly thick one and isn't that old. We had it folded and stored for the past 3 years. I laid it out yesterday and discovered it has about 5-6 holes in it. They are about 1 1/2 inches long and 1/4 inch wide. Not just cuts, but looks like holes. Someone told me to use a tire patch, but I went to the store and the ones I found are self adhesive. I just didn't think they felt that sticky to me and I wondered if the adhesive is safe for fish. I just have no idea how to fix these. I was told to patch both sides of the holes. I do still have some liner scraps leftover, but I don't know what kind of glue to use. Please someone help me save my $400 liner!

I've had good success with generic rubber pond liner patch kits like this one: http://www.homedepot.com/p/Tot...
These are generally self-adhesive, and I always use a solvent to clean the area thoroughly before applying.

I used some tire patches and bought a vulcanizing glue stuff in a small tube. Clean the area and put on the glue and let it dry and then put the patch on. Press to seal. I actually heated it with the hairdryer to help bond it. I have not used it yet IN the pond, so I don't know if this is going to work yet or not. Will post an update later when I know more.
The tire patches btw were only $12 for a box of 20 and the glue was like $4.
I patched both sides of the hole, top and underneath side.

My experienced suggestion is "Pond liner repair by PondPro2000 is a final solution which seals the liner instead of changing it"