These are two different cases of one noun (both in singular form): - 'woda' is nominative (noun is a subject of the sentence like 'Woda jest w szklance' = 'The water is in the glass') - 'wodę' is accusative (noun is a direct object, like "Mam wodę" = 'I have water')
Polish is generally spoken as written when you know the rules. Every letter has its sound and it isn't changed when you are reading whole word. "a" is something like English "ah" and "ę" is something like French "en" eg. in "bien".
ę IS changed when you read the whole word actually, because when at the end of the word (like in wodę) it is pronounced simply as -e, without any nasal quality.
I'd argue that the nasal quality in those situations is diminished, but nonetheless exists. Of course it depends on person, region, attentiveness to detail and exact word and surrounding sounds. I personally like the sound of nasal vowels and try to speak them when appropriate and appreciate people who do. Not counting some exceptions, you'd be perfectly understood without nasality at the end of the word, but sometimes judged as sloppy by language purists.
I no longer hear sound when using Duolingo. The problem has been happening for two days and is not happening with any other app on my phone. So in the 'Type what you hear' exercises I am just guessing.