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I noticed that my turtle ate a few small pebbles, what should I do?

Remove all the small pebbles in the tank and wait for it to poop it out, then retrieve it.

How small do they have to be?

Well, if you've seen how big your turtle poops, then you have a ballpark to look for. If you think it swallowed something bigger, then you might want to consider having them checked out by a vet.