Well, the first picture has roots that look perfect and the second picture looks like they've become desiccated. What is the white material/background in the second picture?

How do you apply your hydroponic nutrients? Does the NFT mean nutrient film technique? Your problem has to be one (or more) of the following: light contacting roots, insufficient oxygen in your nutrient solution, pH of nutrient solution, chemicals in nutrient solution, or pests.

Could you guess on the nutrient solution temperature? If it is too low it will shock the plants, too high and it will not hold the necessary oxygen.
gainesvillegreen Reviewed by gainesvillegreen on . brown roots? but not root rot!!! have nft.canna aqua vega 1.2 cf, ph 5.8, tap water ( been tested ok ). about a week after being put in the tank the roots under rockwool block turn a sort of translucent brown and are weak, but do not go mushy, roots outside of block are white but eventually go the same. plants still take up water, but growth is very slow. stem go's purple and older leaves, then others yellow suggesting slow,or no neut up take. everything is always sterilised and rinsed, but this has happened 3 times in a row. Rating: 5