It's best not to think about the non-water stuff that exists in the water pipes. I once had to open up our 200-litre water heater (which supplies the entire house) to replace the heater coil, and now have to live with the knowledge of what, and how much of it, was inside. "Ignorance is bliss" couldn't be more accurate.
I usually just run vinegar through it every once in a while and then run a few pots of just water to get rid of any residual vinegar. Beware, it'll make the house smell like vinegar for the rest of the day.
White vinegar works, or you can pick up "sour salt" in the Kosher section, which is citric acid and since you don't need much the rest is handy as a substitute for lemon juice. Dilute with plenty of water, run the machine, it removes calcium deposits.