How microwaves work (physics equation version):"The water dipole<sup></sup> attempts to continuously reorient in electromagnetic radiation's oscillating electric field. Dependent on the frequency the dipole may move in time to the field, lag behind it or remain apparently unaffected.
When the dipole lags behind the field then interactions between the dipole and the field leads to an energy loss by heating, the extent of which is dependent on the phase difference of these fields; heating being maximal twice each cycle."
http://www.lsbu.ac.uk/water/microwave.html
Caution. Contains hard science content; may not be comprehendable by naturopaths, homeopaths, Reki practitioners, aura readers and other snake oil salesmen.
Nifty applet demonstrating it all: http://www.colorado.edu/physics/2000/applets/h2o.html