The majority of the dust is vacuumed in through the lenses. As the lens is zoomed in and out air travels through the lens carrying dust particles and deposits them in the mirror box/shutter area. When the shutter is fired the CCD is exposed and dust will gravitate to the CCD.

To avoid dust from entering your camera: use a blower brush on your lenses to remove some of the surface dust.

 

Changing lenses will also allow dust to enter the mirror box area: When changing the lenses face the camera downwards.

 

The dust can be cleaned from the sensor.