Their ship is not far from here in a river.
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What is the relationship between 'here' and 'in a river'? Are they in apposition?
No, it doesn't read that way to me. It seems to be saying that the ship is in a river, not far from here (and "here" is wherever the speaker is standing, but NOT near the ship).
If you want those to be in apposition, try rephrasing as I did above.