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Water molecules are dipolar molecules. This means that they organise their electrons in such a way as to make one side of the molecules positively charged and the other side negatively charged.

Microwaves are actually radio waves in a specific wavelength and frequency band. In microwave ovens this is usually around 12.2 cm and 2.45 GHz. Microwaves (and all other electromagnetic waves) form oscillating electric fields which go from positive to negative and back again in this case 2.45 billion times a second.

Because opposite charges attract and like charges repel and the electric field keeps changing from positive to negative and back again, this forces the water molecules to continuously realign themselves to try and keep up (or more technically to try and minimise the force on their positive and negative poles).

Now this rotational motion causes the molecules to bump into each other increasing their random (movement or) kinetic energy. The random kinetic energy of molecules is another way of decribing heat! So the more kinetic energy the molecules have the hotter the material becomes.

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Q: How do microwaves effect water particles?
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