Sorry! I googled scratched glass repair and found this link for a polisher.
http://www.hobbytool.com/glasspolishingkit.aspx
Only problem is I don't know if the compound used in this would be safe for the little fishies and such. Also, don't know if salt water would wear it down and scratches re-appear over time.(maybe you could contact manufacturer, tell them what you are using it for and see what they say)
Not much help again. Maybe this will at least bump you so someone with the right answer may see it. Good luck!