I would just line the whole thing, up to the rim, rather than trying to make a joint under water. It won't take that much more
pond liner, and you can use cheaper builder's plastic instead if you put some carpet or fabric scrap between the dirt and plastic in the middle, and then an interior liner between plastic and water, perhaps of carpet scraps. This technique is called carpet sandwich (plastic sandwiched between two layers of carpets) and can be used to line any small pond.