When you have the snake out to clean the whole cage you could use lime away. Just be sure to clean it out well. Or you can try vinegar, just put some on a rag or paper towel and let it sit on the spots for a little while then wipe away.
A razor blade can help remove large build up before doing that so it works faster if you have thicker water spots.
After you get it clean, try wiping most of the water off the glass after spraying to prevent more spots. You can also spray with distilled water to prevent spots, just don't fill the water bowl with it.
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