Mattador, I've never stayed at either one, but Slough Creek Campground, of course, sits along the river so it's right where you want to be it sounds like. Both campgrounds are fairly small. They have fire pits, vault toilets and bear boxes. They both fill up quickly due to the nearby fishing. I've never heard how the fishing is at Pebble Creek but I imagine it's good. I've heard the same thing as you on Slough Creek, that the fishing is very good. I have a friend that backpacks into the remote camp sites along the river several miles to the northeast. They make the trip about the 3rd week in July every year and always seem to catch fish.
I know that at Slough Creek only a handful of the sites are in the trees, the rest are out in the open. A few sit right along the river.
Make sure that if anyone in your party is tent camping that you don't bring fishy smelling clothes into your tent.
Enjoy our time in Yellowstone!
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