Occasionally you may run into a Full-screen bug when running Aquaria for the first time. This bug can crash the app.
This problem seems to be more common with Steam's version because it doesn't necessarily run the configuration dialog the first time you run the game.
To avoid it, once you've installed Aquaria, first run the file named AquariaConfig.exe through a run windows app dialog, instead of launching from the Steam menu.
You only need to do this once and set your desired video options.
After that the program should run fine.
The cause of the bug seems to be that when the config dialog is not launched first, the game doesn't auto-detect the correct screen options at start up, causing a problem. Once the config dialog is run the game gets the correct information.