Public toilets are usually only free in government run facilities, such a gallery and museums. Otherwise you will have to pay a, usually 5CZK (so have some coins with you), fee to the attendant - if not a coin operated lock. You can find toilets in all department stores (like Kotva, Myslbek or Tesco).

Most Czech's use McDonalds and other fast food shops for free toilets.

In terms of hygiene, Prague’s public toilets are generally best avoided. I suppose the term “squalid” is an apt description of the conditions you’re likely to find inside. That doesn’t mean we recommend pissing all over the  paved street, although many people do anyway.  Nasty old ladies wait outside of public restrooms at metro stations from 8am to 8pm. In exchange for 5 CZK, they will yield you toilet paper – usually just a tiny scrap. They are often reluctant to give you more unless you throw some extra change down.You will see a lot of the toilet stalls have black lights; that’s to prevent junkies from being able to find a vein, and thus shoot up and pass out in the stalls. In seedier joints, sometimes they’ll just shoot up over the sink in front of everyone. The public restrooms are usually called W.C. (pronounced veh-tseh), toalety, or záchod. If you’re in a restaurant or bar and can’t find it, ask the barman, kde je tady záchod? They’ll point you in the right direction.