Will the EMF be imprinted into the water?

All frequency emission is a form of EMF.
Water will readily absorb any information. So you can’t say it imprints a frequency but not EMF. That is like saying you can smell the air, but not breathe.
3 minutes is all it takes, doesn’t matter if the frequency is low or high.
EMF by itself is not harmful. Certain qualities of EMF can be. Regarding 50 or 60 Hz, it is the constant entrainment of that frequency that makes AC lines harmful to the body. Cellular processes like to run around 30 Hz, and being around a constant 50/60 Hz source will entrain cells to operate above their norm — causing undo stress. It is akin to constantly running instead of taking the time to walk.
50 Hz and 60 Hz by themselves do not cause harm when used in a fashion that is not constant.
If it did you probably would want to sell your sub-woofers and stop listening to music.