Russ, Interesting in such that I have no Muskrats and locally the only thing I have seen within a 20 mile radius is Beavers. Some of the holes are larger than others. Some are as little as 1.5 inches in diameter and others as large as 6 inches. I have some leopard frogs and some very very large bullfrogs ( at least 6 inches in diameter ). I have looked in the past for muskrats and other swimming types of critters but the only animal I have seen swimming on the pond is the odd raccoon that wanders by at night. I have had a few snakes that have poked around in the pond and some that when I get close disappear into nowhere. Maybe they are using the holes.

I had thought it might be old root holes, but in 3 years I doubt that the roots would have decayed enough that it would leave only the hole and nothing else. As the pond starts to dry I find more and more holes in the side ( some only going in an inch or two while others going deeper ) and each time a frog is in the hole.

I have had some spots on the surface where it looks like a mud volcano erupted and there is some wet mud with a hole going straight down under it. Those holes tend to be less than 2 inches in diameter.

I will try to take a few pics tonight to show you what I am seeing. In the mean time any thoughts would be appreciated. I just want to get rid of the critter/critters that are doing this so that I can actually seal up the pond and not have as much seepage as I am right now.

Theo, that was my first thought for the frogs. I know that up north we have frogs that burow deep in the mud to overwinter. Its amazing what they can dig through when they are trying to survive the cold winters. I also notice the deep holes are always about 2 to 3 ft below the pond surface. Which is about hte frost line. The surface holes that I have seen are only shallow ones like what they would use for keeping cool and away from herons over the summer.

Also anyone know of anything to use to fill these holes back in other than the clay they already dug out?

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1/10 - 1/4 acre pond plus 16 ft deep/ Plus 40 ft by 20 ft by 6 ft deep koi and fathead minnow pond next to it. Upstate NY