"Choke" is a tricky word. The main meaning is that the connected noun is unable to breathe. I choke, Bob chokes, we are choking. We can't breathe. However it can also mean that the connected noun causes something else to be unable to breathe. Bob chokes me, smoke chokes me, I can't breathe. When we say "Bob chokes" it normally means Bob can't breathe. However if Bob is a murder and someone asks "how does Bob kill", we could say "Bob chokes". Note the strong context there, making it clear that we mean Bob causes other people to be unable to breathe.
"The water choked" will almost always sound like the water can't breathe. You can say the water choked Bob because you have a clear target for who or what can't breathe. But you should only say "Thing chokes" if (1) Thing is unable to breathe, or (2) you have a clear statement or clear context that Thing is causing a specific other thing to not-breathe.