I had no idea that this could happen. The only time Nix swam was when she decided to dive into a lake out of the blue. She was swimming for no longer than 5 minutes (it's a park lake not meant for swimming, neither dogs nor people) but I don't think she drank any of the water, fortunately. So no problems with her stool afterwards.
Another dog I had (also a GSD), Desi, would swim in the river and fetch sticks. I don't remember any problems with her stool, either.
Maybe you could ask the vet?