if it is an EPDM liner, there are a number of "peel and stick" products intended to repair rubber roof systems. on a dry liner it just takes a little mechanical prep (scrubbing and wiping any crud off) and then essentially it goes on instantly and you are done. the patches themselves can be epdm or some other rubber compound, even sbs/asphalt blends, although those usually come with a granule surface which would look odd when you are done. don't know if there are any that work under water.
i doubt that these would work well for a vinyl/pvc or other plastic liner. i suppose those could be remelted/welded with a patch of similar material, but that's not something i would waste any time on -- the plastic liners aren't very durable, and should probably be replaced.