"There is no water in the glass."
没有 means "does not have". The reverse order becomes more or less "Does not have water in (this) glass", which does not work grammatically.
I'm a little confused with the word order. I thought it would be 杯子没有水里. Can someone please clarify?
The preposition 裡/里 means inside and it relates to the noun directly before it.
杯子裡 = the inside of the cup
沒有水 = has no water
Your word order seems natural following English grammar, it might translate something like "the cup has no the inside of the water."