(If somebody wants to describe it better, be my guest.)
Now that you have this key, go to the screen outside the prison and armory, and there is a wooden pole with a keyhole in near the door leading to the prison. Use the Floodgate Key there, and the gate will close and the water will stop flowing.
NOW go to the organ and play all the notes at once; and then check out the path to the right of the fountain. It should have opened up, and you will be able to get a Rosetta Stone; this path then leads into the locked door of the prison. 🙂