Use ordinary public transport ticket for ferries 
There are 7 public ferries in Prague:
1 
Sedlec-Zamky operates all year round.
2 V Podbabě-Podhoří operates all year round.
3 Lihovar-Veslařský ostrov operates from April till October.
4 Kazín-Černošice operates from June till September.
5 Náplavka Smíchov-Výtoň-Císařská louka operates from April till October.
6 Lanovičky-Nádraží Modřany operates from April till October.
7 Pražská tržnice-Ostrov Štvanice-Rohanský ostrov operates from April till October.
Which one do you use? 
Info: https://pid.cz/jizdni-rady-podle-linek/privozy/
https://www.instagram.com/p/BY5C7OnlF1j/