We've been debating whether or not aquamarine is a compound word or not. To me, I view "aqua" as being just a prefix rather than a standalone word, so I don't think aquamarine would be considered to be a compound word.
It comes from the Latin phrase 'aqua marina' meaning 'water of the sea'. So it would be a compound word, either in Latin or when coined, rather than a prefix.
For it to be a prefix, it would have to be a type of marina, modified to be related to water. It is a gemstone. And all marinas are water related.