I hope this is helpful,1. Don't drink the water in the pond.
In the above sentence, "the" before "water" is required because "the water" is restricted by the phrase "in the pond."
If somebody has a water bottle and s/he attempts to drink some water in the bottle, however, I could say, "Don't drink water in the pond" as a warning, because it is cold in the pond and s/he might catch a cold. Please tell me if my understanding is correct.
I'm not sure how the bottled water fits into this, so I may not understand your question well, but:
If I heard someone say, "Don't drink water in the pond", I might interpret it to mean, 'Don't drink water while you are in the pond.'
If the person said, 'Don't drink water from the pond,' I would assume that, for some reason I shouldn't drink any water from this pond.
2. We are measuring the carbon dioxide in the atmosphere.
I don't know if I should leave out "the" before "carbon" or either will do. I would like to hear native speakers opinion. Unless there is some reason having to do with your experiment, I think either one will do. In order to avoid the problem, one could say, 'We are measuring atmospheric carbon dioxide.'
I have had another question in the same sentence structure, i.e., "the + noun + in."
I like life in the countryside (all one word) better than life in town.
You could also say, 'I like life in the country better than life in town. Here 'the country is understood to stand in opposition to 'town.'
Do I need "the" before "life in the countryside" and "life in town"?
Yes. 'The countryside' is understood to mean a rural area. However, 'Countryside life is better than town life.'
'Countryside picnics are a great pleasure.'
'Country living is my favorite.'
Thank you in advance.