That's true, and that's why you see Bear Grylls drinking his own pee on Man vs. Wild. But the body still breaks down whatever it ingests into its elemental origins. Every substance on earth is a composition of certain elements arranged into a particular molecular structure.
For example, when you sprinkle salt on your fries, you are eating salt, NaCl, which is a molecule. But what your body passes after digestion is not salt, it is sodium and chlorine, Na and Cl, which are elements. You pass whatever excess you don't use up. When you add baking soda to a batch of cookies you are baking, you are eating sodium bicarbonate, NaHCO3, but after digestion you pass sodium, hydrogen, carbon and oxygen. The same goes for other chemical compositions, including anti-depressants.
No, you don't use every bit of what you ingest, and that's why we urinate and go #2. But everything that we pass is found naturally occurring on the planet, and therefore is not harmful as long as you don't have huge amounts of an element in places it doesn't belong. That's why we are having the mercury in tuna problem. What people can add to waste that is potentially dangerous is bacteria and viruses that we carry around and spread to others.