"There is no water in the bottle."
Is the 子 really needed? I am under the impression that Chinese people quite often just use 瓶 for bottle.
Usually, in conversation, 瓶子 is expressed in conversation to help the listeners (including natives) understand the complete vocabulary. Otherwise, if 瓶 is expressed alone without enough context, then some single characters with similar pinyins i.e. 屏 can be possible in the saying.
子 can be neglected either (1) context-wise or (2) as a classifier i.e.