instead of using a liner you could use clay. You would have to get the special type thats called bentonite. I believe its powdery and it expands when water hits it. The frogs would then be able to burrow down into it. In addition I would make the pond deeper its sounds like the pond froze down to bottom (3-4 feet is ideal). Also if you want to make a really great frog habitat make sure there is plenty of vegation and sticks in the water for them to hide out in and to lay their eggs on.

Last year, I found 5 dead frogs in my pond after the winter thaw. Last fall, I left several pots, containing soil, but no plants, submerged in the pond (as well as many plant filled pots). So far, this spring, I have not found any dead frogs, and actually heard 2-3 of them "singing" the other night. Hopefully, unless we get another blast of winter that freezes the pond, I won't have a frog kill this spring. This pond, at the deepest level, is 4' deep. I have a second, tiny pond that I was going to clean out this past weekend, but found that it already has toad? eggs in it.

toads dont breed this time of year they are most likely spring peeper or wood frog eggs.

I agree that you need to put pots of soil in the bottom of your swamp. You could also sink some quilt batting down there, which does a good job of insulating them.

Also, if you had any wide swings of temperatures this winter, that could have killed them. If it gets nice and warm too soon, they come out of hibernation and then don't have time to slow down their metabolism before it gets really cold again. Unfortunately, there's nothing you can do for that. But do put pots with soil and quilt batting down for them next year.