My plant roots have a discoloration of brownish

could it just be the roots being stained from the nuts in the water or could it be root rot and how can i tell, my plants look healthy as all hell.

Hard to say without pics but if the plants are "healthy as all hell" then no matter what it is it is NOT a problem.
If the plant has root rot it will produce new roots as it wants to live as much as you want it to. If it is root rot you can just cut off the dead and dying roots to keep the system clean.