It would be much better to put your nutes through the medium when changing them. Also, letting it run with a product like Flora Kleen for an hour or two every other week would help with all that build up.
If you add fresh water to your res as the plant uses it, add it through the medium as well. Doing this will also help with the build up.
You say you dump the water when it gets low? Don't you end up having to change the nutes like every day? That would seem like a hassle. I use the add back rule. I put 2 1/2 gal worth of nutes in my water farm, and once I have added 2 1/2 gallons to bucket of plain water, I change my nutes. Usually about every week or 10 days.