Recently bought a 97 civic automatic trans. It has 120k miles on it

I'm fairly certain the car was sitting in a few feet of water at one point which got into the transmission as the trans fluid is very dirty and murky (essentially grey) and water like. Shifts rough 1st and 2nd gear.

I'd like to completely drain all the fluid and replace it without doing a 'flush' as I'm worried it might not shift if I did that because I'm not sure how long this water/fluid mixture has been in.

Wondering what is the best possible way to go about this

 

get that crap out of there immediately. flush it, use whatever method you can to remove it ALL. then, put in new fluid, run it a bit, drive a couple miles, and flush it AGAIN. refill with honda z1 or equivalent (ive had good luck with valvoline), and cross your fingers. that generation is not known for particularly good auto transmissions to begin with.