Yes if it's only running through water, it's simply a cooling system problem. If there are any other symptoms that generally leads you to the REAL problem. Missing could mean the cyl is not getting enough compression, which can happen if your head gasket is blown. Which would add pressure to your cooling system which would eventually fill up with air. Not so much leaking antifreeze as it getting forced out.
Just losing antifreeze though, check hoses, cap, radiator, water pump, and the painful but relatively inexpensive heater core(if you don't do the work yourself, you're looking at better than $1000 in labor, and if you do the work yourself you understand why it's way more than that). Check everywhere for leaks. If you can't find any and there's no other symptoms, it's probably the heater core.
I'm a cheap kinda guy. I try replacing the cheapest first and working my way to the expensive stuff.