Hello from Prague,
The truth, if you stick with the swimming pool as your main criteria for a hotel in Prague you won't have a large choice.
Most of the favorite hotels in Prague are in reconstructed historical buildings where it's quite impossible to have such a facility.
For sure you can find some hotels with a swimming pool but you will end up staying out of the historical center of Prague, which is a pity, if I remember well, hotels with a swimming pool are Top Hotel Praha (3*) in Prague 4 or Hotel Praha (5*) in Prague 6.
But you can find many good hotels and apartments in the center of Prague which are close to some wellness centers even with swimming pools.
Apartment King Wenceslas has a wellness center on the ground floor:
http://kingwenceslas.co.uk/apartments-ki…
You can find more hotels and apartments on this website:
http://kingwenceslas.co.uk/
Good luck