Your sentences are dealing with the location of the water, so in a glass is correct.
 
Here is  part of an A to Z preposition dictionary  I have used for my esl writing and speaking classes for  prepositions including  in and with.  It gives  simple definitions and sample sentences or phrases for using them,
 
IN
1. Place thought of as an area:   in London; in Europe
2. Within a location:    in the room; in a building; in a cup / glass
3; large units of time:   That happened in March, in 1992
4.By means of:  write in pencil, speak in English
 
Note there are 9 definitions of  the preposition in in the dictionary  
WITH
1. Accompanying:  He came with her;  I have my keys with me. 
2. Having ; containing:    Here is a book with a map of an island.
3. By means of; using:   I repaired the shoes with glue;   I wrote that  with a pencil
4. Manner:   I did it with ease; with difficulty
 
Depending on context of sentence and the verb used prepositional use is sometimes confusing.
For your sentence see #2  in IN
 
Hope this helps
 
Ron 
 
 
 
 
 
 
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