Recently posted at about.com: a history of spas. On the sidebar: "Possible Origins of the Word 'Spa.'" Everyone sitting down?
• From the Latin words 'Espa' (fountain) and 'Sparsa' (from spargere = to bubble up).
• "Sanus Per Aquam" [S P A] - meaning health by or through water.
• "Solus Per Aqua" [S P A] Latin for enter by means of water. Other interpretation: "health through water."
• “Salut Per Aqua” [S P A] Latin for health or relaxation through water. Found in graffiti in Roman baths
This site mentions the real origin (Spa is a place name in Belgium: cf. OED), and then goes on to mention the above, with minor variations, not much better at the Latin, but at least with references to books that make the various suggestions.
Another suggestion I don't believe--Hungarian...