No it doesn't prevent the medication from doing it's job. But water can aid in flushing out bacteria from your urinary, thus alleviating symptoms.
Does not drinking enough water really make that much of a difference. I guess the question is if I'm not drinking enough water would it prevent the medication from doing its job?
You will just need to head back to your doctor or try using a different doctor to see if the re tests are conclusive. Chlamydia can be pretty tough to treat but not NGU for sure. Drink more water for now.