Our family really enjoyed the Punkva caves.. definitely call in advance to reserve as I was told all weekends in July/Aug were reserved. We had a Friday reservation but at last minute needed to change the day and they had openings! In your GPS, you go to the Tourist information center in the town Skalni Mlyn. Basically there is a hotel, restaurant, some snack kiosks, WC and the Tourist office (green building) and that is it so you can't miss it. Upon arrival we had to pay for parking and then go but our tickets. The tour is only in Czech so don't forget to get the mini-guide in your language so you understand each stop in the cave. And be sure to pay the small fee if you want to take pictures (although no one checked your sticker). You have the option to walk about 30min to the start of the tour or take the 10 min tourist train. If you take the train, you need to buy tickets from a different desk in the info center.
Once you arrive at the entrance there are a few food kiosks, WC and another info desk. You wait in the building until your tour starts. If possible try to get towards the front so you can see what the guide is pointing at. The caves are cold so bring a warm coat and a raincoat, as it is dripping in places. There are 5 stops in the caves before getting in the boat (about 40 min). You walk on wet paths/steps, all with modern handrails, but it is easy for all ages. It is mostly well lit and only for a few minutes in one section was there some loud church music. You will need the flashlight on your phone to read the mini-guide.
We have been on cave tours before but this was unique because of the boat tour. There is also a cool abyss that you visit before boarding the boats. The boat takes about 20min with a stop halfway. You definitely need to watch your head especially if you sit on the outside of the boat benches but that is part of the tour fun. You are dropped off at the starting point again.
All in all just over an hour. Definitely recommended! If the weather was nicer we would have also done the cable car. Beautiful area!