Never heard about running in water??? I usually just hook the motor to 2 d-cell batteries (3 volts), and let em run till the battery dies. You can do the same thing if your charger has motor run feature, set to 3 volts and run a while (until brushes are seated).
I've never heard of breakin in water. I'm familar with cleaning a well used brushed motor by running at low voltage in distilled water. You'd be surprised at how much gunk comes out - use a big shot of nitro cleaner and re-oil everything. Usually used on a motor thats gone downhill in an attempt to get some of it back. I've had mixed results.