need some help here with a root question

my plants are in a 5 gal. bucket with drip holes in bottom set in another 5gal bucket. when i water some water passes thru to the catch bucket. i forgot to empty them and when i did them the roots are coming out of the drip holes and are very long, now sitting in the stagnent water. should i dump the water or will that dry up those roots.

i understand i have a high risk of root rot if i leave them as is right?

so you have a semi hydro?you get root rot if the water is bad,no oxygen in t w