Spa town between prague and vienna

Not much in the way of mineral spas in the south of the country. Take a look at https://www.lazne-lednice.cz/en/spa-treatment/iodine-bromine-water or search more in the Mikulov area.

How are you getting from Prague to Vienna?

Luhačovice in Moravia is famous for its mineral springs and is generally just a lovely spa town with some amazing architecture and great walks. It's primarily visited by Czechs - when I was there, the only other foreigners we saw were Slovaks (it's very close to the border) - which makes it even more interesting.

Radio Prague did a feature on the best spas a while ago that you might find interesting as you plan:
https://english.radio.cz/best-spas-czech-republic-8721557