Why did my Civic overheat at 3am last night?

It sounds like the water was frozen, the engine will heat up quick with no water circulating. But then again, if there was steam coming out of your radiator that would imply that you did have circulation. This could be a few things. First off, you should always use antifreeze. It not only is effective against freezing, it also raises the boiling point to help with cooling in the summer. It also has a lubricant in there for the water pump. You may have inadvertently ruined the water pump if you were running straight water. If not, the thermostat may be defective. Yes I know you said you replaced it but they just go like that sometimes. Another thing to check is the fan, does it kick on while idling? Usually if the fan is not working it is not a big issue if the vehicle is moving because the air flow will keep it cool. If you are just sitting there though while running, it will heat up quick. One easy way to see if you have circulation is to let it run with the cap off and watch the fluid. If it does not move after warming up, take out the thermostat and run the engine again. Does it flow now? If not, chances are the water pump is shot. Hope this helped.